4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>3/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
67 structures with ChimeraX and Pymol in addition to Jmol and
71 <!-- JAL-3829 -->Discover 3D structure data for sequences
72 with Uniprot references via 3D-Beacons
75 <!-- JAL-3391 -->Rank and select available structures for
76 Uniprot sequences according to number of residues in
77 structure mapped to positions involved in the alignment
80 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
81 memory settings at launch
84 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
85 menu for selecting which database to fetch from in sequence
89 <!-- JAL-2226 -->Structure annotation rows for all mapped
90 chains in 3D structures are included in the 'Reference
91 Annotation' for a sequence
94 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
97 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
98 molecules imported from ENA records are shown as RNA
100 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
103 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
107 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
111 <!-- JAL-3530 -->-nowebservicediscovery command line
112 argument to prevent automatic discovery of analysis
113 webservices on launch
116 <!-- JAL-3618 -->Allow 'App' directories to be opened when
117 locating Chimera, ChimeraX or Pymol binaries via filechooser
118 opened by double clicking the Structure Preferences' path
122 <!-- JAL-3837 -->GPL license info on splash screen and About
126 <em>Jalview Native App</em>
129 <!-- JAL- -->New Jalview Develop app - making it even easier
130 to get at Jalview's development builds
133 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
134 and Jalview Develop applications.
137 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
138 Console and other window widgets in taskbar and dock rather
139 than anonymous 'Java' icons
141 </ul> <em>JalviewJS</em>
144 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
148 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
151 <!-- JAL-3163 -->Missing message bundle keys are only
152 reported once per key (avoids excessive log output in js
156 <!-- JAL-3168 -->Feature type is included in the title of
157 the Feature Settings' Colour Chooser dialog
160 </ul> <em>Development</em>
163 <!-- -->First integrated JalviewJS and Jalview release
165 <li>Updated building instructions</li>
167 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
168 process, added support for system package provided eclipse
171 <li>Install4j 9.0.x used for installer packaging</li>
172 <li>Notarized MacOS installer for compatibility with Big
173 Sur and Monterey</li>
175 <!-- JAL-3805 -->Uninstaller application for old
176 (InstallAnywhere based) Jalview installations removed from
180 <!-- JAL-3930 -->Improved use of installers for unattended
181 installation with a customizedId of "JALVIEW" in install4j's
185 <!-- JAL-3907 -->Improved compatibility of Jalview build
186 with Java 17 (next LTS target)
189 <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel used by Jalview
198 <!-- JAL-3674 -->Slow structure commands can block Jalview
202 <!-- JAL-3904 -->Structure window's viewer-specific menu
203 disappears when only one structure is shown (and many
204 sequences:one chain mappings are present)
207 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
208 the first SEQUENCE_GROUP defined
213 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
214 propagated between Linked CDS - Protein alignments and their
215 trees (known defect from 2.11.1.3)
218 <!-- JAL-3761 -->Not all codon positions highlighted for
219 overlapping exon splice sites (e.g due to RNA slippage)
222 <!-- JAL-3794 -->X was not being recognised as the unknown
223 base in DNA sequences
226 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
227 Structure Preferences
230 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
233 <!-- JAL-3162 -->Can edit a feature so that start > end
236 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
237 modified graduated colour
240 <!-- JAL-3788 -->New View with automatic 'Show Overview'
241 preference enabled results in Null Pointer Exceptions when
242 clustal colouring is enabled
245 <!-- JAL-3275 -->Can open multiple Preferences panels
248 <!-- JAL-3949 -->Standard out logging broken: messages only
249 routing to stderr and appear as a raw template
251 </ul> <em>JalviewJS</em>
254 <!-- JAL-3202 -->Consensus profile may include zero (rounded
255 down) percentage values causing a divide by zero
270 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
271 via Info.args when there are arguments on the URL
274 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
277 <!-- JAL-3603 -->Annotation file fails to load from URL in
280 </ul> <em>Development</em>
284 <li>Fixed non-fatal gradle errors during build</li>
286 <!-- JAL-3745 -->Updated build.gradle for use with
296 <td width="60" align="center" nowrap><strong><a
297 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
298 <em>18/01/2022</em></strong></td>
300 <td align="left" valign="top">
303 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
304 updated by Jalview or other applications (Windows, other non
307 </ul> <em>Security</em>
310 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
316 <td width="60" align="center" nowrap><strong><a
317 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
318 <em>6/01/2022</em></strong></td>
320 <td align="left" valign="top"><em>Security</em>
323 <!-- JAL-3934 -->Version bump library dependency: Log4j
330 <td width="60" align="center" nowrap><strong><a
331 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
332 <em>20/12/2021</em></strong></td>
334 <td align="left" valign="top"><em>Security</em>
337 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
339 </ul> <em>Development</em>
341 <li>Updated building instructions</li>
346 <!-- JAL-3840 -->Occupancy calculation is incorrect for
347 alignment columns with over -1+2^32 gaps (breaking filtering
351 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
352 scale factors being set with buggy window-managers (linux
355 </ul> <em>Development</em>
357 <li>Fixed non-fatal gradle errors during build</li>
362 <td width="60" align="center" nowrap><strong><a
363 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
364 <em>09/03/2021</em></strong></td>
365 <td align="left" valign="top"><em>Improved control of
366 Jalview's use of network services via jalview_properties</em>
369 <!-- JAL-3814 -->New .jalview_properties token controlling
370 launch of the news browser (like -nonews argument)
373 <!-- JAL-3813 -->New .jalview_properties token controlling
374 download of linkout URLs from
375 www.jalview.org/services/identifiers
378 <!-- JAL-3812 -->New .jalview_properties token controlling
379 download of BIOJSHTML templates
382 <!-- JAL-3811 -->New 'Discover Web Services' option to
383 trigger a one off JABAWS discovery if autodiscovery was
387 <td align="left" valign="top">
390 <!-- JAL-3818 -->Intermittent deadlock opening structure in
393 </ul> <em>New Known defects</em>
396 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
397 always restored from project (since 2.10.3)
400 <!-- JAL-3806 -->Selections from tree built from CDS aren't
401 propagated to Protein alignment (since 2.11.1.3)
407 <td width="60" align="center" nowrap><strong><a
408 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
409 <em>29/10/2020</em></strong></td>
410 <td align="left" valign="top">
415 <td align="left" valign="top">
418 <!-- JAL-3765 -->Find doesn't always highlight all matching
419 positions in a sequence (bug introduced in 2.11.1.2)
422 <!-- JAL-3760 -->Alignments containing one or more protein
423 sequences can be classed as nucleotide
426 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
427 sequences after alignment of protein products (known defect
428 first reported for 2.11.1.0)
431 <!-- JAL-3725 -->No tooltip or popup menu for genomic
432 features outwith CDS shown overlaid on protein
435 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
436 correctly mapped by Jalview (e.g. affects viral CDS with
437 ribosomal slippage, since 2.9.0)
440 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
444 <!-- JAL-3700 -->Selections in CDS sequence panel don't
445 always select corresponding protein sequences
448 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
449 column selection doesn't always ignore hidden columns
451 </ul> <em>Installer</em>
454 <!-- JAL-3611 -->Space character in Jalview install path on
455 Windows prevents install4j launching getdown
457 </ul> <em>Development</em>
460 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
461 version numbers in doc/building.md
467 <td width="60" align="center" nowrap><strong><a
468 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
469 <em>25/09/2020</em></strong></td>
470 <td align="left" valign="top">
474 <td align="left" valign="top">
477 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
478 "Encountered problems opening
479 https://www.jalview.org/examples/exampleFile_2_7.jvp"
485 <td width="60" align="center" nowrap><strong><a
486 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
487 <em>17/09/2020</em></strong></td>
488 <td align="left" valign="top">
491 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
492 residue in cursor mode
495 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
496 HTSJDK from 2.12 to 2.23
499 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
500 optimisations and improvements suggested by Bob Hanson and
501 improved compatibility with JalviewJS
504 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
505 alignments from Pfam and Rfam
508 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
509 import (no longer based on .gz extension)
512 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
515 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
516 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
520 <!-- JAL-3667 -->Improved warning messages, debug logging
521 and fixed Retry action when Jalview encounters errors when
522 saving or making backup files.
525 <!-- JAL-3676 -->Enhanced Jalview Java Console:
527 <li>Jalview's logging level can be configured</li>
528 <li>Copy to Clipboard Buttion</li>
532 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
533 when running on Linux (Requires Java 11+)
535 </ul> <em>Launching Jalview</em>
538 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
539 through a system property
542 <!-- JAL-3477 -->Improved built-in documentation and command
543 line help for configuring Jalview's memory
547 <td align="left" valign="top">
550 <!-- JAL-3691 -->Conservation and Quality tracks are shown
551 but not calculated and no protein or DNA score models are
552 available for tree/PCA calculation when launched with
553 Turkish language locale
556 <!-- JAL-3493 -->Escape does not clear highlights on the
557 alignment (Since Jalview 2.10.3)
560 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
561 doesn't slide selected sequences, just sequence under cursor
564 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
565 sequence under the cursor
568 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
569 multiple EMBL gene products shown for a single contig
572 <!-- JAL-3696 -->Errors encountered when processing variants
573 from VCF files yield "Error processing VCF: Format specifier
577 <!-- JAL-3697 -->Count of features not shown can be wrong
578 when there are both local and complementary features mapped
579 to the position under the cursor
582 <!-- JAL-3673 -->Sequence ID for reference sequence is
583 clipped when Right align Sequence IDs enabled
586 <!-- JAL-2983 -->Slider with negative range values not
587 rendered correctly in VAqua4 (Since 2.10.4)
590 <!-- JAL-3685 -->Single quotes not displayed correctly in
591 internationalised text for some messages and log output
594 <!-- JAL-3490 -->Find doesn't report matches that span
595 hidden gapped columns
598 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
599 panels, Alignment viewport and annotation renderer.
602 <!-- JAL-3561 -->Jalview ignores file format parameter
603 specifying output format when exporting an alignment via the
607 <!-- JAL-3667 -->Windows 10: For a minority of users, if
608 backups are not enabled, Jalview sometimes fails to
609 overwrite an existing file and raises a warning dialog. (in
610 2.11.0, and 2.11.1.0, the workaround is to try to save the
611 file again, and if that fails, delete the original file and
615 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
619 <!-- JAL-3741 -->References to http://www.jalview.org in
620 program and documentation
622 </ul> <em>Launching Jalview</em>
625 <!-- JAL-3718 -->Jalview application fails when launched the
626 first time for a version that has different jars to the
627 previous launched version.
629 </ul> <em>Developing Jalview</em>
632 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
633 data, causing cloverReport gradle task to fail with an
637 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
638 monitor the release channel
640 </ul> <em>New Known defects</em>
643 <!-- JAL-3748 -->CDS shown in result of submitting proteins
644 in a CDS/Protein alignment to a web service is wrong when
645 proteins share a common transcript sequence (e.g. genome of
649 <!-- JAL-3576 -->Co-located features exported and
650 re-imported are ordered differently when shown on alignment
651 and in tooltips. (Also affects v2.11.1.0)
654 <!-- JAL-3702 -->Drag and drop of alignment file onto
655 alignment window when in a HiDPI scaled mode in Linux only
656 works for the top left quadrant of the alignment window
659 <!-- JAL-3701 -->Stale build data in jalview standalone jar
660 builds (only affects 2.11.1.1 branch)
663 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
664 when alignment view restored from project (since Jalview
668 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
669 protein products for certain ENA records are repeatedly
670 shown via Calculate->Show Cross Refs
676 <td width="60" align="center" nowrap><strong><a
677 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
678 <em>22/04/2020</em></strong></td>
679 <td align="left" valign="top">
682 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
683 'virtual' codon features shown on protein (or vice versa)
684 for display in alignments, on structure views (including
685 transfer to UCSF chimera), in feature reports and for
689 <!-- JAL-3121 -->Feature attributes from VCF files can be
690 exported and re-imported as GFF3 files
693 <!-- JAL-3376 -->Capture VCF "fixed column" values
694 POS, ID, QUAL, FILTER as Feature Attributes
697 <!-- JAL-3375 -->More robust VCF numeric data field
698 validation while parsing
701 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
705 <!-- JAL-3535 -->Feature Settings dialog title includes name
709 <!-- JAL-3538 -->Font anti-aliasing in alignment views
713 <!-- JAL-3468 -->Very long feature descriptions truncated in
717 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
718 with no feature types visible
721 <!-- JAL-3574 -->Improved support for filtering feature
722 attributes with large integer values
725 <em>Jalview Installer</em>
728 <!-- JAL-3449 -->Versions for install4j and getdown and
729 installer template version reported in console (may be null
730 when Jalview launched as executable jar or via conda)
733 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
734 higher quality background images
737 <!-- JAL-3394 -->New installer/application launcher
738 generated with install4j 8.0.4
741 <!-- JAL-3420 -->Jalview File Associations shown for Unix
745 <!-- JAL-3477 -->Improved defaults for maximum memory
746 setting when running on large memory machines
748 </ul> <em>Release processes</em>
751 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
754 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
755 access to test-release channel builds
757 </ul> <em>Build System</em>
760 <!-- JAL-3510 -->Clover updated to 4.4.1
763 <!-- JAL-3513 -->Test code included in Clover coverage
766 </ul> <em>Groovy Scripts</em>
769 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
770 to stdout containing the consensus sequence for each
771 alignment in a Jalview session
774 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
775 genomic sequence_variant annotation from CDS as
776 missense_variant or synonymous_variant on protein products.
780 <td align="left" valign="top">
783 <!-- JAL-3581 -->Hidden sequence markers still visible when
784 'Show hidden markers' option is not ticked
787 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
788 PNG output when 'Automatically set ID width' is set in
789 jalview preferences or properties file
792 <!-- JAL-3571 -->Feature Editor dialog can be opened when
793 'Show Sequence Features' option is not ticked
796 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
797 buttons in Feature Settings dialog are clicked when no
801 <!-- JAL-3412 -->ID margins for CDS and Protein views not
802 equal when split frame is first opened
805 <!-- JAL-3296 -->Sequence position numbers in status bar not
806 correct after editing a sequence's start position
809 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
810 with annotation and exceptions thrown when only a few
811 columns shown in wrapped mode
814 <!-- JAL-3386 -->Sequence IDs missing in headless export of
815 wrapped alignment figure with annotations
818 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
819 ID fails with ClassCastException
822 <!-- JAL-3389 -->Chimera session not restored from Jalview
826 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
827 feature settings dialog also selects columns
830 <!-- JAL-3473 -->SpinnerNumberModel causes
831 IllegalArgumentException in some circumstances
834 <!-- JAL-3534 -->Multiple feature settings dialogs can be
838 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
839 alignment window is closed
842 <!-- JAL-3406 -->Credits missing some authors in Jalview
843 help documentation for 2.11.0 release
846 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
847 includes Pfam ID as sequence's accession rather than its
850 </ul> <em>Java 11 Compatibility issues</em>
853 <!-- JAL-2987 -->OSX - Can't view some search results in
854 PDB/Uniprot search panel
856 </ul> <em>Installer</em>
859 <!-- JAL-3447 -->Jalview should not create file associations
860 for 3D structure files (.pdb, .mmcif. .cif)
862 </ul> <em>Repository and Source Release</em>
865 <!-- JAL-3474 -->removed obsolete .cvsignore files from
869 <!-- JAL-3541 -->Clover report generation running out of
872 </ul> <em>New Known Issues</em>
875 <!-- JAL-3523 -->OSX - Current working directory not
876 preserved when Jalview.app launched with parameters from
880 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
881 clipped in headless figure export when Right Align option
885 <!-- JAL-3542 -->Jalview Installation type always reports
886 'Source' in console output
889 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
890 on jalview's bamboo server but run fine locally.
896 <td width="60" align="center" nowrap><strong><a
897 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
898 <td align="left" valign="top">
901 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
902 Application and Installers built with <a
903 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
904 (licensed to the Jalview open source project) rather than
908 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
909 memory settings, receive over the air updates and launch
910 specific versions via (<a
911 href="https://github.com/threerings/getdown">Three
915 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
916 for formats supported by Jalview (including .jvp project
920 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
921 line arguments and switch between different getdown channels
924 <!-- JAL-3141 -->Backup files created when saving Jalview
925 project or alignment files
929 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
933 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
934 updated to version 2.12.0
937 <!-- JAL-2620 -->Alternative genetic code tables for
941 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
943 <li><strong>Enhanced visualisation and analysis
944 of Sequence Features</strong>
947 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
948 implementation that allows updates) used for Sequence
952 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
953 features can be filtered and shaded according to any
954 associated attributes (e.g. variant attributes from VCF
955 file, or key-value pairs imported from column 9 of GFF
959 <!-- JAL-2879 -->Feature Attributes and shading schemes
960 stored and restored from Jalview Projects
963 <!-- JAL-3334 -->Use full Sequence Ontology (via
964 BioJava) to recognise variant features
967 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
968 on peptide sequences (also coloured red by default)
971 <!-- JAL-2792 -->Popup window to show full report for a
972 selected sequence feature's details
975 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
976 sequence feature render algorithm (Z-sort/transparency
980 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
985 <!-- JAL-3205 -->Symmetric score matrices for faster tree
988 <li><strong>Principal Components Analysis Viewer</strong>
991 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
992 results and Viewer state saved in Jalview Project
995 <!-- JAL-2962 -->'Change parameters' option removed from
996 viewer's drop-down menus
999 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1000 PCA image incrementally
1003 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1007 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1009 <li><strong>Speed and Efficiency</strong>
1012 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1013 selections and multiple groups when working with large
1017 <!-- JAL-3200 -->Speedier import of annotation rows when
1018 parsing Stockholm files
1021 <li><strong>User Interface</strong>
1024 <!-- JAL-2933 -->Finder panel remembers last position in
1028 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1029 (What you see is what is shown)<br />Only visible
1030 regions of alignment are shown by default (can be
1031 changed in user preferences)
1034 <!-- JAL-3169 -->File Chooser stays open after
1035 responding Cancel to the Overwrite Dialog
1038 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1039 when all sequences are hidden
1042 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1043 selection region, and gap count when inserting or
1047 <!-- JAL-3132 -->Status bar updates over sequence and
1051 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1052 shown when in wrapped mode
1055 <!-- JAL-3073 -->Can select columns by dragging
1056 left/right in a graph or histogram annotation
1059 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1063 <!-- JAL-2621 -->Cursor changes over draggable box in
1067 <!-- JAL-3181 -->Consistent ordering of links in
1068 sequence id popup menu
1071 <!-- JAL-3080 -->Red line indicating tree-cut position
1072 not shown if no subgroups are created
1075 <!-- JAL-3042 -->Removed ability to configure length of
1076 search history by right-clicking search box
1082 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1085 <li><strong>Java 11 Support (not yet on general
1089 <!-- -->OSX GUI integrations for App menu's 'About'
1090 entry and trapping CMD-Q
1093 </ul> <em>Deprecations</em>
1096 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1097 capabilities removed from the Jalview Desktop
1100 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1101 and unmarshalling has been replaced by JAXB for Jalview
1102 projects and XML based data retrieval clients
1105 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1109 <!-- -->Jalview Desktop no longer distributed via Java Web
1112 </ul> <em>Documentation</em>
1115 <!-- JAL-3003 -->Added remarks about transparent rendering
1116 effects not supported in EPS figure export
1119 <!-- JAL-2903 -->Typos in documentation for Preferences
1122 </ul> <em>Development and Release Processes</em>
1125 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1129 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1130 keys in Message bundles
1133 <!-- JAL-3225 -->Eclipse project configuration managed with
1137 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1138 continuous integration for unattended Test Suite execution
1141 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1145 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1149 <!-- JAL-3248 -->Developer documentation migrated to
1150 markdown (with HTML rendering)
1153 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1156 <!-- JAL-3289 -->New URLs for publishing development
1161 <td align="left" valign="top">
1164 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1167 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1168 superposition in Jmol fail on Windows
1171 <!-- JAL-3286 -->Blank error dialog is displayed when
1172 discovering structures for sequences with lots of PDB
1176 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1177 with monospaced font
1180 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1181 Jalview project involving multiple views
1184 <!-- JAL-3164 -->Overview for complementary view in a linked
1185 CDS/Protein alignment is not updated when Hide Columns by
1186 Annotation dialog hides columns
1189 <!-- JAL-3158 -->Selection highlighting in the complement of
1190 a CDS/Protein alignment stops working after making a
1191 selection in one view, then making another selection in the
1195 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1199 <!-- JAL-3154 -->Table Columns could be re-ordered in
1200 Feature Settings and Jalview Preferences panels
1203 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1204 redrawing the overview with large alignments
1207 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1208 region if columns were selected by dragging right-to-left
1209 and the mouse moved to the left of the first column
1212 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1213 a hidden column marker via scale popup menu
1216 <!-- JAL-2846 -->Error message for trying to load in invalid
1217 URLs doesn't tell users the invalid URL
1220 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1224 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1225 during show cross references or Fetch Database References
1226 are shown in red in original view
1229 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1230 correctly on peptide sequence (computed variant shown as
1234 <!-- JAL-2060 -->'Graduated colour' option not offered for
1235 manually created features (where feature score is Float.NaN)
1238 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1239 printed when columns are hidden
1242 <!-- JAL-3082 -->Regular expression error for '(' in Select
1243 Columns by Annotation description
1246 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1247 dragging out of Scale or Annotation Panel
1250 <!-- JAL-3075 -->Column selection incorrect after scrolling
1254 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1258 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1262 <!-- JAL-3002 -->Column display is out by one after Page
1263 Down, Page Up in wrapped mode
1266 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1269 <!-- JAL-2932 -->Finder searches in minimised alignments
1272 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1273 selected on opening an alignment
1276 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1280 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1281 when different groups in the alignment are selected
1284 <!-- JAL-2717 -->Internationalised colour scheme names not
1285 shown correctly in menu
1288 <!-- JAL-3206 -->Colour by Annotation can go black at
1289 min/max threshold limit
1292 <!-- JAL-3125 -->Value input for graduated feature colour
1293 threshold gets 'unrounded'
1296 <!-- JAL-2982 -->PCA image export doesn't respect background
1300 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1304 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1307 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1308 alignment, not Tree font
1311 <!-- JAL-2964 -->Associate Tree with All Views not restored
1315 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1316 Overview shown in complementary view
1319 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1320 shown without normalisation
1323 <!-- JAL-3021 -->Sequence Details report should open
1324 positioned at top of report
1327 <!-- JAL-914 -->Help page can be opened twice
1330 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1333 </ul> <em>Editing</em>
1336 <!-- JAL-2822 -->Start and End should be updated when
1337 sequence data at beginning or end of alignment added/removed
1341 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1342 doesn't relocate sequence features correctly when start of
1343 sequence is removed (Known defect since 2.10)
1346 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1347 Sequence dialog corrupts dataset sequence
1350 <!-- JAL-868 -->Structure colours not updated when
1351 associated tree repartitions the alignment view (Regression
1354 </ul> <em>Datamodel</em>
1357 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1358 sequence's End is greater than its length
1360 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1364 <!-- JAL-3288 -->Menus work properly in split-screen
1366 </ul> <em>New Known Defects</em>
1369 <!-- JAL-3340 -->Select columns containing feature by double
1370 clicking ignores bounds of an existing selected region
1373 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1374 gapped regions of protein alignment.
1377 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1378 PCA View is restored from a Jalview 2.11 project
1381 <!-- JAL-3213 -->Alignment panel height can be too small
1385 <!-- JAL-3240 -->Display is incorrect after removing gapped
1386 columns within hidden columns
1389 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1390 re-enters window after dragging left to select columns to
1391 left of visible region
1394 <!-- JAL-2876 -->Features coloured according to their
1395 description string and thresholded by score in earlier
1396 versions of Jalview are not shown as thresholded features in
1397 2.11. To workaround please create a Score filter instead.
1400 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1401 reset group visibility
1404 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1405 linked CDS/Protein view
1408 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1409 alignments with multiple views can close views unexpectedly
1411 </ul> <em>Java 11 Specific defects</em>
1414 <!-- JAL-3235 -->Jalview Properties file is not sorted
1415 alphabetically when saved
1421 <td width="60" nowrap>
1422 <div align="center">
1423 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1426 <td><div align="left">
1430 <!-- JAL-3101 -->Default memory for Jalview webstart and
1431 InstallAnywhere increased to 1G.
1434 <!-- JAL-247 -->Hidden sequence markers and representative
1435 sequence bolding included when exporting alignment as EPS,
1436 SVG, PNG or HTML. <em>Display is configured via the
1437 Format menu, or for command-line use via a Jalview
1438 properties file.</em>
1441 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1442 API and sequence data now imported as JSON.
1445 <!-- JAL-3065 -->Change in recommended way of starting
1446 Jalview via a Java command line: add jars in lib directory
1447 to CLASSPATH, rather than via the deprecated java.ext.dirs
1451 <em>Development</em>
1454 <!-- JAL-3047 -->Support added to execute test suite
1455 instrumented with <a href="http://openclover.org/">Open
1460 <td><div align="left">
1464 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1465 row shown in Feredoxin Structure alignment view of example
1469 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1470 annotation displayed.
1473 <!-- JAL-3107 -->Group conservation/consensus not shown
1474 for newly created group when 'Apply to all groups'
1478 <!-- JAL-3087 -->Corrupted display when switching to
1479 wrapped mode when sequence panel's vertical scrollbar is
1483 <!-- JAL-3003 -->Alignment is black in exported EPS file
1484 when sequences are selected in exported view.</em>
1487 <!-- JAL-3059 -->Groups with different coloured borders
1488 aren't rendered with correct colour.
1491 <!-- JAL-3092 -->Jalview could hang when importing certain
1492 types of knotted RNA secondary structure.
1495 <!-- JAL-3095 -->Sequence highlight and selection in
1496 trimmed VARNA 2D structure is incorrect for sequences that
1500 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1501 annotation when columns are inserted into an alignment,
1502 and when exporting as Stockholm flatfile.
1505 <!-- JAL-3053 -->Jalview annotation rows containing upper
1506 and lower-case 'E' and 'H' do not automatically get
1507 treated as RNA secondary structure.
1510 <!-- JAL-3106 -->.jvp should be used as default extension
1511 (not .jar) when saving a Jalview project file.
1514 <!-- JAL-3105 -->Mac Users: closing a window correctly
1515 transfers focus to previous window on OSX
1518 <em>Java 10 Issues Resolved</em>
1521 <!-- JAL-2988 -->OSX - Can't save new files via the File
1522 or export menus by typing in a name into the Save dialog
1526 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1527 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1528 'look and feel' which has improved compatibility with the
1529 latest version of OSX.
1535 <td width="60" nowrap>
1536 <div align="center">
1537 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1538 <em>7/06/2018</em></strong>
1541 <td><div align="left">
1545 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1546 annotation retrieved from Uniprot
1549 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1550 onto the Jalview Desktop
1554 <td><div align="left">
1558 <!-- JAL-3017 -->Cannot import features with multiple
1559 variant elements (blocks import of some Uniprot records)
1562 <!-- JAL-2997 -->Clustal files with sequence positions in
1563 right-hand column parsed correctly
1566 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1567 not alignment area in exported graphic
1570 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1571 window has input focus
1574 <!-- JAL-2992 -->Annotation panel set too high when
1575 annotation added to view (Windows)
1578 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1579 network connectivity is poor
1582 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1583 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1584 the currently open URL and links from a page viewed in
1585 Firefox or Chrome on Windows is now fully supported. If
1586 you are using Edge, only links in the page can be
1587 dragged, and with Internet Explorer, only the currently
1588 open URL in the browser can be dropped onto Jalview.</em>
1591 <em>New Known Defects</em>
1594 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1601 <td width="60" nowrap>
1602 <div align="center">
1603 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1606 <td><div align="left">
1610 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1611 for disabling automatic superposition of multiple
1612 structures and open structures in existing views
1615 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1616 ID and annotation area margins can be click-dragged to
1620 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1624 <!-- JAL-2759 -->Improved performance for large alignments
1625 and lots of hidden columns
1628 <!-- JAL-2593 -->Improved performance when rendering lots
1629 of features (particularly when transparency is disabled)
1632 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1633 for exchange of Jalview features and Chimera attributes
1634 made generally available
1638 <td><div align="left">
1641 <!-- JAL-2899 -->Structure and Overview aren't updated
1642 when Colour By Annotation threshold slider is adjusted
1645 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1646 overlapping alignment panel
1649 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1653 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1654 improved: CDS not handled correctly if transcript has no
1658 <!-- JAL-2321 -->Secondary structure and temperature
1659 factor annotation not added to sequence when local PDB
1660 file associated with it by drag'n'drop or structure
1664 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1665 dialog doesn't import PDB files dropped on an alignment
1668 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1669 scroll bar doesn't work for some CDS/Protein views
1672 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1673 Java 1.8u153 onwards and Java 1.9u4+.
1676 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1677 columns in annotation row
1680 <!-- JAL-2913 -->Preferences panel's ID Width control is
1681 not honored in batch mode
1684 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1685 for structures added to existing Jmol view
1688 <!-- JAL-2223 -->'View Mappings' includes duplicate
1689 entries after importing project with multiple views
1692 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1693 protein sequences via SIFTS from associated PDB entries
1694 with negative residue numbers or missing residues fails
1697 <!-- JAL-2952 -->Exception when shading sequence with
1698 negative Temperature Factor values from annotated PDB
1699 files (e.g. as generated by CONSURF)
1702 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1703 tooltip doesn't include a text description of mutation
1706 <!-- JAL-2922 -->Invert displayed features very slow when
1707 structure and/or overview windows are also shown
1710 <!-- JAL-2954 -->Selecting columns from highlighted
1711 regions very slow for alignments with large numbers of
1715 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1716 with 'StringIndexOutOfBounds'
1719 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1720 Feel for OSX platforms running Java 10
1723 <!-- JAL-2960 -->Adding a structure to existing structure
1724 view appears to do nothing because the view is hidden
1725 behind the alignment view
1731 <!-- JAL-2926 -->Copy consensus sequence option in applet
1732 should copy the group consensus when popup is opened on it
1738 <!-- JAL-2913 -->Fixed ID width preference is not
1742 <em>New Known Defects</em>
1745 <!-- JAL-2973 --> Exceptions occasionally raised when
1746 editing a large alignment and overview is displayed
1749 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1750 repeatedly after a series of edits even when the overview
1751 is no longer reflecting updates
1754 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1755 structures for protein subsequence (if 'Trim Retrieved
1756 Sequences' enabled) or Ensembl isoforms (Workaround in
1757 2.10.4 is to fail back to N&W mapping)
1760 <!-- JAL-2990 -->Export Annotations from File Menu with
1761 CSV option gives blank output
1767 <td width="60" nowrap>
1768 <div align="center">
1769 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1770 <em>24/1/2018</em></strong>
1773 <td><div align="left">
1775 <li>Updated Certum Codesigning Certificate (Valid till
1776 30th November 2018)</li>
1779 <td><div align="left">
1784 <!-- JAL-2859-->Only one structure is loaded when
1785 several sequences and structures are selected for
1789 <!-- JAL-2851-->Alignment doesn't appear to scroll
1790 vertically via trackpad and scrollwheel
1793 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1794 in cursor mode when cursor lies in hidden region at
1798 <!-- JAL-2827-->Helix annotation has 'notches' when
1799 scrolled into view if columns are hidden
1802 <!-- JAL-2740-->Annotation column filter can be slow to
1803 reset (ie after hitting cancel) for large numbers of
1807 <!-- JAL-2849-->User preference for disabling inclusion
1808 of sequence limits when exporting as flat file has no
1812 <!-- JAL-2679-->Reproducible cross-reference
1813 relationships when retrieving sequences from
1820 <td width="60" nowrap>
1821 <div align="center">
1822 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1825 <td><div align="left">
1829 <!-- JAL-2446 -->Faster and more efficient management and
1830 rendering of sequence features
1833 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1834 429 rate limit request hander
1837 <!-- JAL-2773 -->Structure views don't get updated unless
1838 their colours have changed
1841 <!-- JAL-2495 -->All linked sequences are highlighted for
1842 a structure mousover (Jmol) or selection (Chimera)
1845 <!-- JAL-2790 -->'Cancel' button in progress bar for
1846 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1849 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1850 view from Ensembl locus cross-references
1853 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1857 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1858 feature can be disabled
1861 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1862 PDB easier retrieval of sequences for lists of IDs
1865 <!-- JAL-2758 -->Short names for sequences retrieved from
1871 <li>Groovy interpreter updated to 2.4.12</li>
1872 <li>Example groovy script for generating a matrix of
1873 percent identity scores for current alignment.</li>
1875 <em>Testing and Deployment</em>
1878 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1882 <td><div align="left">
1886 <!-- JAL-2643 -->Pressing tab after updating the colour
1887 threshold text field doesn't trigger an update to the
1891 <!-- JAL-2682 -->Race condition when parsing sequence ID
1895 <!-- JAL-2608 -->Overview windows are also closed when
1896 alignment window is closed
1899 <!-- JAL-2548 -->Export of features doesn't always respect
1903 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1904 takes a long time in Cursor mode
1910 <!-- JAL-2777 -->Structures with whitespace chainCode
1911 cannot be viewed in Chimera
1914 <!-- JAL-2728 -->Protein annotation panel too high in
1918 <!-- JAL-2757 -->Can't edit the query after the server
1919 error warning icon is shown in Uniprot and PDB Free Text
1923 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1926 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1929 <!-- JAL-2739 -->Hidden column marker in last column not
1930 rendered when switching back from Wrapped to normal view
1933 <!-- JAL-2768 -->Annotation display corrupted when
1934 scrolling right in unwapped alignment view
1937 <!-- JAL-2542 -->Existing features on subsequence
1938 incorrectly relocated when full sequence retrieved from
1942 <!-- JAL-2733 -->Last reported memory still shown when
1943 Desktop->Show Memory is unticked (OSX only)
1946 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1947 features of same type and group to be selected for
1951 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1952 alignments when hidden columns are present
1955 <!-- JAL-2392 -->Jalview freezes when loading and
1956 displaying several structures
1959 <!-- JAL-2732 -->Black outlines left after resizing or
1963 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1964 within the Jalview desktop on OSX
1967 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1968 when in wrapped alignment mode
1971 <!-- JAL-2636 -->Scale mark not shown when close to right
1972 hand end of alignment
1975 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1976 each selected sequence do not have correct start/end
1980 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1981 after canceling the Alignment Window's Font dialog
1984 <!-- JAL-2036 -->Show cross-references not enabled after
1985 restoring project until a new view is created
1988 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1989 URL links appears when only default EMBL-EBI link is
1990 configured (since 2.10.2b2)
1993 <!-- JAL-2775 -->Overview redraws whole window when box
1994 position is adjusted
1997 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1998 in a multi-chain structure when viewing alignment
1999 involving more than one chain (since 2.10)
2002 <!-- JAL-2811 -->Double residue highlights in cursor mode
2003 if new selection moves alignment window
2006 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2007 arrow key in cursor mode to pass hidden column marker
2010 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2011 that produces correctly annotated transcripts and products
2014 <!-- JAL-2776 -->Toggling a feature group after first time
2015 doesn't update associated structure view
2018 <em>Applet</em><br />
2021 <!-- JAL-2687 -->Concurrent modification exception when
2022 closing alignment panel
2025 <em>BioJSON</em><br />
2028 <!-- JAL-2546 -->BioJSON export does not preserve
2029 non-positional features
2032 <em>New Known Issues</em>
2035 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2036 sequence features correctly (for many previous versions of
2040 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2041 using cursor in wrapped panel other than top
2044 <!-- JAL-2791 -->Select columns containing feature ignores
2045 graduated colour threshold
2048 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2049 always preserve numbering and sequence features
2052 <em>Known Java 9 Issues</em>
2055 <!-- JAL-2902 -->Groovy Console very slow to open and is
2056 not responsive when entering characters (Webstart, Java
2063 <td width="60" nowrap>
2064 <div align="center">
2065 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2066 <em>2/10/2017</em></strong>
2069 <td><div align="left">
2070 <em>New features in Jalview Desktop</em>
2073 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2077 <!-- JAL-2745 -->HTTPS used for all connections to
2082 <td><div align="left"></div></td>
2085 <td width="60" nowrap>
2086 <div align="center">
2087 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2088 <em>7/9/2017</em></strong>
2091 <td><div align="left">
2095 <!-- JAL-2588 -->Show gaps in overview window by colouring
2096 in grey (sequences used to be coloured grey, and gaps were
2100 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2104 <!-- JAL-2587 -->Overview updates immediately on increase
2105 in size and progress bar shown as higher resolution
2106 overview is recalculated
2111 <td><div align="left">
2115 <!-- JAL-2664 -->Overview window redraws every hidden
2116 column region row by row
2119 <!-- JAL-2681 -->duplicate protein sequences shown after
2120 retrieving Ensembl crossrefs for sequences from Uniprot
2123 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2124 format setting is unticked
2127 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2128 if group has show boxes format setting unticked
2131 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2132 autoscrolling whilst dragging current selection group to
2133 include sequences and columns not currently displayed
2136 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2137 assemblies are imported via CIF file
2140 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2141 displayed when threshold or conservation colouring is also
2145 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2149 <!-- JAL-2673 -->Jalview continues to scroll after
2150 dragging a selected region off the visible region of the
2154 <!-- JAL-2724 -->Cannot apply annotation based
2155 colourscheme to all groups in a view
2158 <!-- JAL-2511 -->IDs don't line up with sequences
2159 initially after font size change using the Font chooser or
2166 <td width="60" nowrap>
2167 <div align="center">
2168 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2171 <td><div align="left">
2172 <em>Calculations</em>
2176 <!-- JAL-1933 -->Occupancy annotation row shows number of
2177 ungapped positions in each column of the alignment.
2180 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2181 a calculation dialog box
2184 <!-- JAL-2379 -->Revised implementation of PCA for speed
2185 and memory efficiency (~30x faster)
2188 <!-- JAL-2403 -->Revised implementation of sequence
2189 similarity scores as used by Tree, PCA, Shading Consensus
2190 and other calculations
2193 <!-- JAL-2416 -->Score matrices are stored as resource
2194 files within the Jalview codebase
2197 <!-- JAL-2500 -->Trees computed on Sequence Feature
2198 Similarity may have different topology due to increased
2205 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2206 model for alignments and groups
2209 <!-- JAL-384 -->Custom shading schemes created via groovy
2216 <!-- JAL-2526 -->Efficiency improvements for interacting
2217 with alignment and overview windows
2220 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2224 <!-- JAL-2388 -->Hidden columns and sequences can be
2228 <!-- JAL-2611 -->Click-drag in visible area allows fine
2229 adjustment of visible position
2233 <em>Data import/export</em>
2236 <!-- JAL-2535 -->Posterior probability annotation from
2237 Stockholm files imported as sequence associated annotation
2240 <!-- JAL-2507 -->More robust per-sequence positional
2241 annotation input/output via stockholm flatfile
2244 <!-- JAL-2533 -->Sequence names don't include file
2245 extension when importing structure files without embedded
2246 names or PDB accessions
2249 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2250 format sequence substitution matrices
2253 <em>User Interface</em>
2256 <!-- JAL-2447 --> Experimental Features Checkbox in
2257 Desktop's Tools menu to hide or show untested features in
2261 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2262 via Overview or sequence motif search operations
2265 <!-- JAL-2547 -->Amend sequence features dialog box can be
2266 opened by double clicking gaps within sequence feature
2270 <!-- JAL-1476 -->Status bar message shown when not enough
2271 aligned positions were available to create a 3D structure
2275 <em>3D Structure</em>
2278 <!-- JAL-2430 -->Hidden regions in alignment views are not
2279 coloured in linked structure views
2282 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2283 file-based command exchange
2286 <!-- JAL-2375 -->Structure chooser automatically shows
2287 Cached Structures rather than querying the PDBe if
2288 structures are already available for sequences
2291 <!-- JAL-2520 -->Structures imported via URL are cached in
2292 the Jalview project rather than downloaded again when the
2293 project is reopened.
2296 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2297 to transfer Chimera's structure attributes as Jalview
2298 features, and vice-versa (<strong>Experimental
2302 <em>Web Services</em>
2305 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2308 <!-- JAL-2335 -->Filter non-standard amino acids and
2309 nucleotides when submitting to AACon and other MSA
2313 <!-- JAL-2316, -->URLs for viewing database
2314 cross-references provided by identifiers.org and the
2315 EMBL-EBI's MIRIAM DB
2322 <!-- JAL-2344 -->FileFormatI interface for describing and
2323 identifying file formats (instead of String constants)
2326 <!-- JAL-2228 -->FeatureCounter script refactored for
2327 efficiency when counting all displayed features (not
2328 backwards compatible with 2.10.1)
2331 <em>Example files</em>
2334 <!-- JAL-2631 -->Graduated feature colour style example
2335 included in the example feature file
2338 <em>Documentation</em>
2341 <!-- JAL-2339 -->Release notes reformatted for readability
2342 with the built-in Java help viewer
2345 <!-- JAL-1644 -->Find documentation updated with 'search
2346 sequence description' option
2352 <!-- JAL-2485, -->External service integration tests for
2353 Uniprot REST Free Text Search Client
2356 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2359 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2364 <td><div align="left">
2365 <em>Calculations</em>
2368 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2369 matrix - C->R should be '-3'<br />Old matrix restored
2370 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2372 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2373 Jalview's treatment of gaps in PCA and substitution matrix
2374 based Tree calculations.<br /> <br />In earlier versions
2375 of Jalview, gaps matching gaps were penalised, and gaps
2376 matching non-gaps penalised even more. In the PCA
2377 calculation, gaps were actually treated as non-gaps - so
2378 different costs were applied, which meant Jalview's PCAs
2379 were different to those produced by SeqSpace.<br />Jalview
2380 now treats gaps in the same way as SeqSpace (ie it scores
2381 them as 0). <br /> <br />Enter the following in the
2382 Groovy console to restore pre-2.10.2 behaviour:<br />
2383 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2384 // for 2.10.1 mode <br />
2385 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2386 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2387 these settings will affect all subsequent tree and PCA
2388 calculations (not recommended)</em></li>
2390 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2391 scaling of branch lengths for trees computed using
2392 Sequence Feature Similarity.
2395 <!-- JAL-2377 -->PCA calculation could hang when
2396 generating output report when working with highly
2397 redundant alignments
2400 <!-- JAL-2544 --> Sort by features includes features to
2401 right of selected region when gaps present on right-hand
2405 <em>User Interface</em>
2408 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2409 doesn't reselect a specific sequence's associated
2410 annotation after it was used for colouring a view
2413 <!-- JAL-2419 -->Current selection lost if popup menu
2414 opened on a region of alignment without groups
2417 <!-- JAL-2374 -->Popup menu not always shown for regions
2418 of an alignment with overlapping groups
2421 <!-- JAL-2310 -->Finder double counts if both a sequence's
2422 name and description match
2425 <!-- JAL-2370 -->Hiding column selection containing two
2426 hidden regions results in incorrect hidden regions
2429 <!-- JAL-2386 -->'Apply to all groups' setting when
2430 changing colour does not apply Conservation slider value
2434 <!-- JAL-2373 -->Percentage identity and conservation menu
2435 items do not show a tick or allow shading to be disabled
2438 <!-- JAL-2385 -->Conservation shading or PID threshold
2439 lost when base colourscheme changed if slider not visible
2442 <!-- JAL-2547 -->Sequence features shown in tooltip for
2443 gaps before start of features
2446 <!-- JAL-2623 -->Graduated feature colour threshold not
2447 restored to UI when feature colour is edited
2450 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2451 a time when scrolling vertically in wrapped mode.
2454 <!-- JAL-2630 -->Structure and alignment overview update
2455 as graduate feature colour settings are modified via the
2459 <!-- JAL-2034 -->Overview window doesn't always update
2460 when a group defined on the alignment is resized
2463 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2464 wrapped view result in positional status updates
2468 <!-- JAL-2563 -->Status bar doesn't show position for
2469 ambiguous amino acid and nucleotide symbols
2472 <!-- JAL-2602 -->Copy consensus sequence failed if
2473 alignment included gapped columns
2476 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2477 widgets don't permanently disappear
2480 <!-- JAL-2503 -->Cannot select or filter quantitative
2481 annotation that are shown only as column labels (e.g.
2482 T-Coffee column reliability scores)
2485 <!-- JAL-2594 -->Exception thrown if trying to create a
2486 sequence feature on gaps only
2489 <!-- JAL-2504 -->Features created with 'New feature'
2490 button from a Find inherit previously defined feature type
2491 rather than the Find query string
2494 <!-- JAL-2423 -->incorrect title in output window when
2495 exporting tree calculated in Jalview
2498 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2499 and then revealing them reorders sequences on the
2503 <!-- JAL-964 -->Group panel in sequence feature settings
2504 doesn't update to reflect available set of groups after
2505 interactively adding or modifying features
2508 <!-- JAL-2225 -->Sequence Database chooser unusable on
2512 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2513 only excluded gaps in current sequence and ignored
2520 <!-- JAL-2421 -->Overview window visible region moves
2521 erratically when hidden rows or columns are present
2524 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2525 Structure Viewer's colour menu don't correspond to
2529 <!-- JAL-2405 -->Protein specific colours only offered in
2530 colour and group colour menu for protein alignments
2533 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2534 reflect currently selected view or group's shading
2538 <!-- JAL-2624 -->Feature colour thresholds not respected
2539 when rendered on overview and structures when opacity at
2543 <!-- JAL-2589 -->User defined gap colour not shown in
2544 overview when features overlaid on alignment
2547 <!-- JAL-2567 -->Feature settings for different views not
2548 recovered correctly from Jalview project file
2551 <!-- JAL-2256 -->Feature colours in overview when first
2552 opened (automatically via preferences) are different to
2553 the main alignment panel
2556 <em>Data import/export</em>
2559 <!-- JAL-2576 -->Very large alignments take a long time to
2563 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2564 added after a sequence was imported are not written to
2568 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2569 when importing RNA secondary structure via Stockholm
2572 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2573 not shown in correct direction for simple pseudoknots
2576 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2577 with lightGray or darkGray via features file (but can
2581 <!-- JAL-2383 -->Above PID colour threshold not recovered
2582 when alignment view imported from project
2585 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2586 structure and sequences extracted from structure files
2587 imported via URL and viewed in Jmol
2590 <!-- JAL-2520 -->Structures loaded via URL are saved in
2591 Jalview Projects rather than fetched via URL again when
2592 the project is loaded and the structure viewed
2595 <em>Web Services</em>
2598 <!-- JAL-2519 -->EnsemblGenomes example failing after
2599 release of Ensembl v.88
2602 <!-- JAL-2366 -->Proxy server address and port always
2603 appear enabled in Preferences->Connections
2606 <!-- JAL-2461 -->DAS registry not found exceptions
2607 removed from console output
2610 <!-- JAL-2582 -->Cannot retrieve protein products from
2611 Ensembl by Peptide ID
2614 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2615 created from SIFTs, and spurious 'Couldn't open structure
2616 in Chimera' errors raised after April 2017 update (problem
2617 due to 'null' string rather than empty string used for
2618 residues with no corresponding PDB mapping).
2621 <em>Application UI</em>
2624 <!-- JAL-2361 -->User Defined Colours not added to Colour
2628 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2629 case' residues (button in colourscheme editor debugged and
2630 new documentation and tooltips added)
2633 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2634 doesn't restore group-specific text colour thresholds
2637 <!-- JAL-2243 -->Feature settings panel does not update as
2638 new features are added to alignment
2641 <!-- JAL-2532 -->Cancel in feature settings reverts
2642 changes to feature colours via the Amend features dialog
2645 <!-- JAL-2506 -->Null pointer exception when attempting to
2646 edit graduated feature colour via amend features dialog
2650 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2651 selection menu changes colours of alignment views
2654 <!-- JAL-2426 -->Spurious exceptions in console raised
2655 from alignment calculation workers after alignment has
2659 <!-- JAL-1608 -->Typo in selection popup menu - Create
2660 groups now 'Create Group'
2663 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2664 Create/Undefine group doesn't always work
2667 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2668 shown again after pressing 'Cancel'
2671 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2672 adjusts start position in wrap mode
2675 <!-- JAL-2563 -->Status bar doesn't show positions for
2676 ambiguous amino acids
2679 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2680 CDS/Protein view after CDS sequences added for aligned
2684 <!-- JAL-2592 -->User defined colourschemes called 'User
2685 Defined' don't appear in Colours menu
2691 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2692 score models doesn't always result in an updated PCA plot
2695 <!-- JAL-2442 -->Features not rendered as transparent on
2696 overview or linked structure view
2699 <!-- JAL-2372 -->Colour group by conservation doesn't
2703 <!-- JAL-2517 -->Hitting Cancel after applying
2704 user-defined colourscheme doesn't restore original
2711 <!-- JAL-2314 -->Unit test failure:
2712 jalview.ws.jabaws.RNAStructExportImport setup fails
2715 <!-- JAL-2307 -->Unit test failure:
2716 jalview.ws.sifts.SiftsClientTest due to compatibility
2717 problems with deep array comparison equality asserts in
2718 successive versions of TestNG
2721 <!-- JAL-2479 -->Relocated StructureChooserTest and
2722 ParameterUtilsTest Unit tests to Network suite
2725 <em>New Known Issues</em>
2728 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2729 phase after a sequence motif find operation
2732 <!-- JAL-2550 -->Importing annotation file with rows
2733 containing just upper and lower case letters are
2734 interpreted as WUSS RNA secondary structure symbols
2737 <!-- JAL-2590 -->Cannot load and display Newick trees
2738 reliably from eggnog Ortholog database
2741 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2742 containing features of type Highlight' when 'B' is pressed
2743 to mark columns containing highlighted regions.
2746 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2747 doesn't always add secondary structure annotation.
2752 <td width="60" nowrap>
2753 <div align="center">
2754 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2757 <td><div align="left">
2761 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2762 for all consensus calculations
2765 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2768 <li>Updated Jalview's Certum code signing certificate
2771 <em>Application</em>
2774 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2775 set of database cross-references, sorted alphabetically
2778 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2779 from database cross references. Users with custom links
2780 will receive a <a href="webServices/urllinks.html#warning">warning
2781 dialog</a> asking them to update their preferences.
2784 <!-- JAL-2287-->Cancel button and escape listener on
2785 dialog warning user about disconnecting Jalview from a
2789 <!-- JAL-2320-->Jalview's Chimera control window closes if
2790 the Chimera it is connected to is shut down
2793 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2794 columns menu item to mark columns containing highlighted
2795 regions (e.g. from structure selections or results of a
2799 <!-- JAL-2284-->Command line option for batch-generation
2800 of HTML pages rendering alignment data with the BioJS
2810 <!-- JAL-2286 -->Columns with more than one modal residue
2811 are not coloured or thresholded according to percent
2812 identity (first observed in Jalview 2.8.2)
2815 <!-- JAL-2301 -->Threonine incorrectly reported as not
2819 <!-- JAL-2318 -->Updates to documentation pages (above PID
2820 threshold, amino acid properties)
2823 <!-- JAL-2292 -->Lower case residues in sequences are not
2824 reported as mapped to residues in a structure file in the
2828 <!--JAL-2324 -->Identical features with non-numeric scores
2829 could be added multiple times to a sequence
2832 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2833 bond features shown as two highlighted residues rather
2834 than a range in linked structure views, and treated
2835 correctly when selecting and computing trees from features
2838 <!-- JAL-2281-->Custom URL links for database
2839 cross-references are matched to database name regardless
2844 <em>Application</em>
2847 <!-- JAL-2282-->Custom URL links for specific database
2848 names without regular expressions also offer links from
2852 <!-- JAL-2315-->Removing a single configured link in the
2853 URL links pane in Connections preferences doesn't actually
2854 update Jalview configuration
2857 <!-- JAL-2272-->CTRL-Click on a selected region to open
2858 the alignment area popup menu doesn't work on El-Capitan
2861 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2862 files with similarly named sequences if dropped onto the
2866 <!-- JAL-2312 -->Additional mappings are shown for PDB
2867 entries where more chains exist in the PDB accession than
2868 are reported in the SIFTS file
2871 <!-- JAL-2317-->Certain structures do not get mapped to
2872 the structure view when displayed with Chimera
2875 <!-- JAL-2317-->No chains shown in the Chimera view
2876 panel's View->Show Chains submenu
2879 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2880 work for wrapped alignment views
2883 <!--JAL-2197 -->Rename UI components for running JPred
2884 predictions from 'JNet' to 'JPred'
2887 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2888 corrupted when annotation panel vertical scroll is not at
2889 first annotation row
2892 <!--JAL-2332 -->Attempting to view structure for Hen
2893 lysozyme results in a PDB Client error dialog box
2896 <!-- JAL-2319 -->Structure View's mapping report switched
2897 ranges for PDB and sequence for SIFTS
2900 SIFTS 'Not_Observed' residues mapped to non-existant
2904 <!-- <em>New Known Issues</em>
2911 <td width="60" nowrap>
2912 <div align="center">
2913 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2914 <em>25/10/2016</em></strong>
2917 <td><em>Application</em>
2919 <li>3D Structure chooser opens with 'Cached structures'
2920 view if structures already loaded</li>
2921 <li>Progress bar reports models as they are loaded to
2922 structure views</li>
2928 <li>Colour by conservation always enabled and no tick
2929 shown in menu when BLOSUM or PID shading applied</li>
2930 <li>FER1_ARATH and FER2_ARATH labels were switched in
2931 example sequences/projects/trees</li>
2933 <em>Application</em>
2935 <li>Jalview projects with views of local PDB structure
2936 files saved on Windows cannot be opened on OSX</li>
2937 <li>Multiple structure views can be opened and superposed
2938 without timeout for structures with multiple models or
2939 multiple sequences in alignment</li>
2940 <li>Cannot import or associated local PDB files without a
2941 PDB ID HEADER line</li>
2942 <li>RMSD is not output in Jmol console when superposition
2944 <li>Drag and drop of URL from Browser fails for Linux and
2945 OSX versions earlier than El Capitan</li>
2946 <li>ENA client ignores invalid content from ENA server</li>
2947 <li>Exceptions are not raised in console when ENA client
2948 attempts to fetch non-existent IDs via Fetch DB Refs UI
2950 <li>Exceptions are not raised in console when a new view
2951 is created on the alignment</li>
2952 <li>OSX right-click fixed for group selections: CMD-click
2953 to insert/remove gaps in groups and CTRL-click to open group
2956 <em>Build and deployment</em>
2958 <li>URL link checker now copes with multi-line anchor
2961 <em>New Known Issues</em>
2963 <li>Drag and drop from URL links in browsers do not work
2970 <td width="60" nowrap>
2971 <div align="center">
2972 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2975 <td><em>General</em>
2978 <!-- JAL-2124 -->Updated Spanish translations.
2981 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2982 for importing structure data to Jalview. Enables mmCIF and
2986 <!-- JAL-192 --->Alignment ruler shows positions relative to
2990 <!-- JAL-2202 -->Position/residue shown in status bar when
2991 mousing over sequence associated annotation
2994 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2998 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2999 '()', canonical '[]' and invalid '{}' base pair populations
3003 <!-- JAL-2092 -->Feature settings popup menu options for
3004 showing or hiding columns containing a feature
3007 <!-- JAL-1557 -->Edit selected group by double clicking on
3008 group and sequence associated annotation labels
3011 <!-- JAL-2236 -->Sequence name added to annotation label in
3012 select/hide columns by annotation and colour by annotation
3016 </ul> <em>Application</em>
3019 <!-- JAL-2050-->Automatically hide introns when opening a
3020 gene/transcript view
3023 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3027 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3028 structure mappings with the EMBL-EBI PDBe SIFTS database
3031 <!-- JAL-2079 -->Updated download sites used for Rfam and
3032 Pfam sources to xfam.org
3035 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3038 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3039 over sequences in Jalview
3042 <!-- JAL-2027-->Support for reverse-complement coding
3043 regions in ENA and EMBL
3046 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3047 for record retrieval via ENA rest API
3050 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3054 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3055 groovy script execution
3058 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3059 alignment window's Calculate menu
3062 <!-- JAL-1812 -->Allow groovy scripts that call
3063 Jalview.getAlignFrames() to run in headless mode
3066 <!-- JAL-2068 -->Support for creating new alignment
3067 calculation workers from groovy scripts
3070 <!-- JAL-1369 --->Store/restore reference sequence in
3074 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3075 associations are now saved/restored from project
3078 <!-- JAL-1993 -->Database selection dialog always shown
3079 before sequence fetcher is opened
3082 <!-- JAL-2183 -->Double click on an entry in Jalview's
3083 database chooser opens a sequence fetcher
3086 <!-- JAL-1563 -->Free-text search client for UniProt using
3087 the UniProt REST API
3090 <!-- JAL-2168 -->-nonews command line parameter to prevent
3091 the news reader opening
3094 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3095 querying stored in preferences
3098 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3102 <!-- JAL-1977-->Tooltips shown on database chooser
3105 <!-- JAL-391 -->Reverse complement function in calculate
3106 menu for nucleotide sequences
3109 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3110 and feature counts preserves alignment ordering (and
3111 debugged for complex feature sets).
3114 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3115 viewing structures with Jalview 2.10
3118 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3119 genome, transcript CCDS and gene ids via the Ensembl and
3120 Ensembl Genomes REST API
3123 <!-- JAL-2049 -->Protein sequence variant annotation
3124 computed for 'sequence_variant' annotation on CDS regions
3128 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3132 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3133 Ref Fetcher fails to match, or otherwise updates sequence
3134 data from external database records.
3137 <!-- JAL-2154 -->Revised Jalview Project format for
3138 efficient recovery of sequence coding and alignment
3139 annotation relationships.
3141 </ul> <!-- <em>Applet</em>
3152 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3156 <!-- JAL-2018-->Export features in Jalview format (again)
3157 includes graduated colourschemes
3160 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3161 working with big alignments and lots of hidden columns
3164 <!-- JAL-2053-->Hidden column markers not always rendered
3165 at right of alignment window
3168 <!-- JAL-2067 -->Tidied up links in help file table of
3172 <!-- JAL-2072 -->Feature based tree calculation not shown
3176 <!-- JAL-2075 -->Hidden columns ignored during feature
3177 based tree calculation
3180 <!-- JAL-2065 -->Alignment view stops updating when show
3181 unconserved enabled for group on alignment
3184 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3188 <!-- JAL-2146 -->Alignment column in status incorrectly
3189 shown as "Sequence position" when mousing over
3193 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3194 hidden columns present
3197 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3198 user created annotation added to alignment
3201 <!-- JAL-1841 -->RNA Structure consensus only computed for
3202 '()' base pair annotation
3205 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3206 in zero scores for all base pairs in RNA Structure
3210 <!-- JAL-2174-->Extend selection with columns containing
3214 <!-- JAL-2275 -->Pfam format writer puts extra space at
3215 beginning of sequence
3218 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3222 <!-- JAL-2238 -->Cannot create groups on an alignment from
3223 from a tree when t-coffee scores are shown
3226 <!-- JAL-1836,1967 -->Cannot import and view PDB
3227 structures with chains containing negative resnums (4q4h)
3230 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3234 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3235 to Clustal, PIR and PileUp output
3238 <!-- JAL-2008 -->Reordering sequence features that are
3239 not visible causes alignment window to repaint
3242 <!-- JAL-2006 -->Threshold sliders don't work in
3243 graduated colour and colour by annotation row for e-value
3244 scores associated with features and annotation rows
3247 <!-- JAL-1797 -->amino acid physicochemical conservation
3248 calculation should be case independent
3251 <!-- JAL-2173 -->Remove annotation also updates hidden
3255 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3256 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3257 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3260 <!-- JAL-2065 -->Null pointer exceptions and redraw
3261 problems when reference sequence defined and 'show
3262 non-conserved' enabled
3265 <!-- JAL-1306 -->Quality and Conservation are now shown on
3266 load even when Consensus calculation is disabled
3269 <!-- JAL-1932 -->Remove right on penultimate column of
3270 alignment does nothing
3273 <em>Application</em>
3276 <!-- JAL-1552-->URLs and links can't be imported by
3277 drag'n'drop on OSX when launched via webstart (note - not
3278 yet fixed for El Capitan)
3281 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3282 output when running on non-gb/us i18n platforms
3285 <!-- JAL-1944 -->Error thrown when exporting a view with
3286 hidden sequences as flat-file alignment
3289 <!-- JAL-2030-->InstallAnywhere distribution fails when
3293 <!-- JAL-2080-->Jalview very slow to launch via webstart
3294 (also hotfix for 2.9.0b2)
3297 <!-- JAL-2085 -->Cannot save project when view has a
3298 reference sequence defined
3301 <!-- JAL-1011 -->Columns are suddenly selected in other
3302 alignments and views when revealing hidden columns
3305 <!-- JAL-1989 -->Hide columns not mirrored in complement
3306 view in a cDNA/Protein splitframe
3309 <!-- JAL-1369 -->Cannot save/restore representative
3310 sequence from project when only one sequence is
3314 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3315 in Structure Chooser
3318 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3319 structure consensus didn't refresh annotation panel
3322 <!-- JAL-1962 -->View mapping in structure view shows
3323 mappings between sequence and all chains in a PDB file
3326 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3327 dialogs format columns correctly, don't display array
3328 data, sort columns according to type
3331 <!-- JAL-1975 -->Export complete shown after destination
3332 file chooser is cancelled during an image export
3335 <!-- JAL-2025 -->Error when querying PDB Service with
3336 sequence name containing special characters
3339 <!-- JAL-2024 -->Manual PDB structure querying should be
3343 <!-- JAL-2104 -->Large tooltips with broken HTML
3344 formatting don't wrap
3347 <!-- JAL-1128 -->Figures exported from wrapped view are
3348 truncated so L looks like I in consensus annotation
3351 <!-- JAL-2003 -->Export features should only export the
3352 currently displayed features for the current selection or
3356 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3357 after fetching cross-references, and restoring from
3361 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3362 followed in the structure viewer
3365 <!-- JAL-2163 -->Titles for individual alignments in
3366 splitframe not restored from project
3369 <!-- JAL-2145 -->missing autocalculated annotation at
3370 trailing end of protein alignment in transcript/product
3371 splitview when pad-gaps not enabled by default
3374 <!-- JAL-1797 -->amino acid physicochemical conservation
3378 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3379 article has been read (reopened issue due to
3380 internationalisation problems)
3383 <!-- JAL-1960 -->Only offer PDB structures in structure
3384 viewer based on sequence name, PDB and UniProt
3389 <!-- JAL-1976 -->No progress bar shown during export of
3393 <!-- JAL-2213 -->Structures not always superimposed after
3394 multiple structures are shown for one or more sequences.
3397 <!-- JAL-1370 -->Reference sequence characters should not
3398 be replaced with '.' when 'Show unconserved' format option
3402 <!-- JAL-1823 -->Cannot specify chain code when entering
3403 specific PDB id for sequence
3406 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3407 'Export hidden sequences' is enabled, but 'export hidden
3408 columns' is disabled.
3411 <!--JAL-2026-->Best Quality option in structure chooser
3412 selects lowest rather than highest resolution structures
3416 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3417 to sequence mapping in 'View Mappings' report
3420 <!-- JAL-2284 -->Unable to read old Jalview projects that
3421 contain non-XML data added after Jalvew wrote project.
3424 <!-- JAL-2118 -->Newly created annotation row reorders
3425 after clicking on it to create new annotation for a
3429 <!-- JAL-1980 -->Null Pointer Exception raised when
3430 pressing Add on an orphaned cut'n'paste window.
3432 <!-- may exclude, this is an external service stability issue JAL-1941
3433 -- > RNA 3D structure not added via DSSR service</li> -->
3438 <!-- JAL-2151 -->Incorrect columns are selected when
3439 hidden columns present before start of sequence
3442 <!-- JAL-1986 -->Missing dependencies on applet pages
3446 <!-- JAL-1947 -->Overview pixel size changes when
3447 sequences are hidden in applet
3450 <!-- JAL-1996 -->Updated instructions for applet
3451 deployment on examples pages.
3458 <td width="60" nowrap>
3459 <div align="center">
3460 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3461 <em>16/10/2015</em></strong>
3464 <td><em>General</em>
3466 <li>Time stamps for signed Jalview application and applet
3471 <em>Application</em>
3473 <li>Duplicate group consensus and conservation rows
3474 shown when tree is partitioned</li>
3475 <li>Erratic behaviour when tree partitions made with
3476 multiple cDNA/Protein split views</li>
3482 <td width="60" nowrap>
3483 <div align="center">
3484 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3485 <em>8/10/2015</em></strong>
3488 <td><em>General</em>
3490 <li>Updated Spanish translations of localized text for
3492 </ul> <em>Application</em>
3494 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3495 <li>Signed OSX InstallAnywhere installer<br></li>
3496 <li>Support for per-sequence based annotations in BioJSON</li>
3497 </ul> <em>Applet</em>
3499 <li>Split frame example added to applet examples page</li>
3500 </ul> <em>Build and Deployment</em>
3503 <!-- JAL-1888 -->New ant target for running Jalview's test
3511 <li>Mapping of cDNA to protein in split frames
3512 incorrect when sequence start > 1</li>
3513 <li>Broken images in filter column by annotation dialog
3515 <li>Feature colours not parsed from features file</li>
3516 <li>Exceptions and incomplete link URLs recovered when
3517 loading a features file containing HTML tags in feature
3521 <em>Application</em>
3523 <li>Annotations corrupted after BioJS export and
3525 <li>Incorrect sequence limits after Fetch DB References
3526 with 'trim retrieved sequences'</li>
3527 <li>Incorrect warning about deleting all data when
3528 deleting selected columns</li>
3529 <li>Patch to build system for shipping properly signed
3530 JNLP templates for webstart launch</li>
3531 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3532 unreleased structures for download or viewing</li>
3533 <li>Tab/space/return keystroke operation of EMBL-PDBe
3534 fetcher/viewer dialogs works correctly</li>
3535 <li>Disabled 'minimise' button on Jalview windows
3536 running on OSX to workaround redraw hang bug</li>
3537 <li>Split cDNA/Protein view position and geometry not
3538 recovered from jalview project</li>
3539 <li>Initial enabled/disabled state of annotation menu
3540 sorter 'show autocalculated first/last' corresponds to
3542 <li>Restoring of Clustal, RNA Helices and T-Coffee
3543 color schemes from BioJSON</li>
3547 <li>Reorder sequences mirrored in cDNA/Protein split
3549 <li>Applet with Jmol examples not loading correctly</li>
3555 <td><div align="center">
3556 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3558 <td><em>General</em>
3560 <li>Linked visualisation and analysis of DNA and Protein
3563 <li>Translated cDNA alignments shown as split protein
3564 and DNA alignment views</li>
3565 <li>Codon consensus annotation for linked protein and
3566 cDNA alignment views</li>
3567 <li>Link cDNA or Protein product sequences by loading
3568 them onto Protein or cDNA alignments</li>
3569 <li>Reconstruct linked cDNA alignment from aligned
3570 protein sequences</li>
3573 <li>Jmol integration updated to Jmol v14.2.14</li>
3574 <li>Import and export of Jalview alignment views as <a
3575 href="features/bioJsonFormat.html">BioJSON</a></li>
3576 <li>New alignment annotation file statements for
3577 reference sequences and marking hidden columns</li>
3578 <li>Reference sequence based alignment shading to
3579 highlight variation</li>
3580 <li>Select or hide columns according to alignment
3582 <li>Find option for locating sequences by description</li>
3583 <li>Conserved physicochemical properties shown in amino
3584 acid conservation row</li>
3585 <li>Alignments can be sorted by number of RNA helices</li>
3586 </ul> <em>Application</em>
3588 <li>New cDNA/Protein analysis capabilities
3590 <li>Get Cross-References should open a Split Frame
3591 view with cDNA/Protein</li>
3592 <li>Detect when nucleotide sequences and protein
3593 sequences are placed in the same alignment</li>
3594 <li>Split cDNA/Protein views are saved in Jalview
3599 <li>Use REST API to talk to Chimera</li>
3600 <li>Selected regions in Chimera are highlighted in linked
3601 Jalview windows</li>
3603 <li>VARNA RNA viewer updated to v3.93</li>
3604 <li>VARNA views are saved in Jalview Projects</li>
3605 <li>Pseudoknots displayed as Jalview RNA annotation can
3606 be shown in VARNA</li>
3608 <li>Make groups for selection uses marked columns as well
3609 as the active selected region</li>
3611 <li>Calculate UPGMA and NJ trees using sequence feature
3613 <li>New Export options
3615 <li>New Export Settings dialog to control hidden
3616 region export in flat file generation</li>
3618 <li>Export alignment views for display with the <a
3619 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3621 <li>Export scrollable SVG in HTML page</li>
3622 <li>Optional embedding of BioJSON data when exporting
3623 alignment figures to HTML</li>
3625 <li>3D structure retrieval and display
3627 <li>Free text and structured queries with the PDBe
3629 <li>PDBe Search API based discovery and selection of
3630 PDB structures for a sequence set</li>
3634 <li>JPred4 employed for protein secondary structure
3636 <li>Hide Insertions menu option to hide unaligned columns
3637 for one or a group of sequences</li>
3638 <li>Automatically hide insertions in alignments imported
3639 from the JPred4 web server</li>
3640 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3641 system on OSX<br />LGPL libraries courtesy of <a
3642 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3644 <li>changed 'View nucleotide structure' submenu to 'View
3645 VARNA 2D Structure'</li>
3646 <li>change "View protein structure" menu option to "3D
3649 </ul> <em>Applet</em>
3651 <li>New layout for applet example pages</li>
3652 <li>New parameters to enable SplitFrame view
3653 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3654 <li>New example demonstrating linked viewing of cDNA and
3655 Protein alignments</li>
3656 </ul> <em>Development and deployment</em>
3658 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3659 <li>Include installation type and git revision in build
3660 properties and console log output</li>
3661 <li>Jalview Github organisation, and new github site for
3662 storing BioJsMSA Templates</li>
3663 <li>Jalview's unit tests now managed with TestNG</li>
3666 <!-- <em>General</em>
3668 </ul> --> <!-- issues resolved --> <em>Application</em>
3670 <li>Escape should close any open find dialogs</li>
3671 <li>Typo in select-by-features status report</li>
3672 <li>Consensus RNA secondary secondary structure
3673 predictions are not highlighted in amber</li>
3674 <li>Missing gap character in v2.7 example file means
3675 alignment appears unaligned when pad-gaps is not enabled</li>
3676 <li>First switch to RNA Helices colouring doesn't colour
3677 associated structure views</li>
3678 <li>ID width preference option is greyed out when auto
3679 width checkbox not enabled</li>
3680 <li>Stopped a warning dialog from being shown when
3681 creating user defined colours</li>
3682 <li>'View Mapping' in structure viewer shows sequence
3683 mappings for just that viewer's sequences</li>
3684 <li>Workaround for superposing PDB files containing
3685 multiple models in Chimera</li>
3686 <li>Report sequence position in status bar when hovering
3687 over Jmol structure</li>
3688 <li>Cannot output gaps as '.' symbols with Selection ->
3689 output to text box</li>
3690 <li>Flat file exports of alignments with hidden columns
3691 have incorrect sequence start/end</li>
3692 <li>'Aligning' a second chain to a Chimera structure from
3694 <li>Colour schemes applied to structure viewers don't
3695 work for nucleotide</li>
3696 <li>Loading/cut'n'pasting an empty or invalid file leads
3697 to a grey/invisible alignment window</li>
3698 <li>Exported Jpred annotation from a sequence region
3699 imports to different position</li>
3700 <li>Space at beginning of sequence feature tooltips shown
3701 on some platforms</li>
3702 <li>Chimera viewer 'View | Show Chain' menu is not
3704 <li>'New View' fails with a Null Pointer Exception in
3705 console if Chimera has been opened</li>
3706 <li>Mouseover to Chimera not working</li>
3707 <li>Miscellaneous ENA XML feature qualifiers not
3709 <li>NPE in annotation renderer after 'Extract Scores'</li>
3710 <li>If two structures in one Chimera window, mouseover of
3711 either sequence shows on first structure</li>
3712 <li>'Show annotations' options should not make
3713 non-positional annotations visible</li>
3714 <li>Subsequence secondary structure annotation not shown
3715 in right place after 'view flanking regions'</li>
3716 <li>File Save As type unset when current file format is
3718 <li>Save as '.jar' option removed for saving Jalview
3720 <li>Colour by Sequence colouring in Chimera more
3722 <li>Cannot 'add reference annotation' for a sequence in
3723 several views on same alignment</li>
3724 <li>Cannot show linked products for EMBL / ENA records</li>
3725 <li>Jalview's tooltip wraps long texts containing no
3727 </ul> <em>Applet</em>
3729 <li>Jmol to JalviewLite mouseover/link not working</li>
3730 <li>JalviewLite can't import sequences with ID
3731 descriptions containing angle brackets</li>
3732 </ul> <em>General</em>
3734 <li>Cannot export and reimport RNA secondary structure
3735 via jalview annotation file</li>
3736 <li>Random helix colour palette for colour by annotation
3737 with RNA secondary structure</li>
3738 <li>Mouseover to cDNA from STOP residue in protein
3739 translation doesn't work.</li>
3740 <li>hints when using the select by annotation dialog box</li>
3741 <li>Jmol alignment incorrect if PDB file has alternate CA
3743 <li>FontChooser message dialog appears to hang after
3744 choosing 1pt font</li>
3745 <li>Peptide secondary structure incorrectly imported from
3746 annotation file when annotation display text includes 'e' or
3748 <li>Cannot set colour of new feature type whilst creating
3750 <li>cDNA translation alignment should not be sequence
3751 order dependent</li>
3752 <li>'Show unconserved' doesn't work for lower case
3754 <li>Nucleotide ambiguity codes involving R not recognised</li>
3755 </ul> <em>Deployment and Documentation</em>
3757 <li>Applet example pages appear different to the rest of
3758 www.jalview.org</li>
3759 </ul> <em>Application Known issues</em>
3761 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3762 <li>Misleading message appears after trying to delete
3764 <li>Jalview icon not shown in dock after InstallAnywhere
3765 version launches</li>
3766 <li>Fetching EMBL reference for an RNA sequence results
3767 fails with a sequence mismatch</li>
3768 <li>Corrupted or unreadable alignment display when
3769 scrolling alignment to right</li>
3770 <li>ArrayIndexOutOfBoundsException thrown when remove
3771 empty columns called on alignment with ragged gapped ends</li>
3772 <li>auto calculated alignment annotation rows do not get
3773 placed above or below non-autocalculated rows</li>
3774 <li>Jalview dekstop becomes sluggish at full screen in
3775 ultra-high resolution</li>
3776 <li>Cannot disable consensus calculation independently of
3777 quality and conservation</li>
3778 <li>Mouseover highlighting between cDNA and protein can
3779 become sluggish with more than one splitframe shown</li>
3780 </ul> <em>Applet Known Issues</em>
3782 <li>Core PDB parsing code requires Jmol</li>
3783 <li>Sequence canvas panel goes white when alignment
3784 window is being resized</li>
3790 <td><div align="center">
3791 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3793 <td><em>General</em>
3795 <li>Updated Java code signing certificate donated by
3797 <li>Features and annotation preserved when performing
3798 pairwise alignment</li>
3799 <li>RNA pseudoknot annotation can be
3800 imported/exported/displayed</li>
3801 <li>'colour by annotation' can colour by RNA and
3802 protein secondary structure</li>
3803 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3804 post-hoc with 2.9 release</em>)
3807 </ul> <em>Application</em>
3809 <li>Extract and display secondary structure for sequences
3810 with 3D structures</li>
3811 <li>Support for parsing RNAML</li>
3812 <li>Annotations menu for layout
3814 <li>sort sequence annotation rows by alignment</li>
3815 <li>place sequence annotation above/below alignment
3818 <li>Output in Stockholm format</li>
3819 <li>Internationalisation: improved Spanish (es)
3821 <li>Structure viewer preferences tab</li>
3822 <li>Disorder and Secondary Structure annotation tracks
3823 shared between alignments</li>
3824 <li>UCSF Chimera launch and linked highlighting from
3826 <li>Show/hide all sequence associated annotation rows for
3827 all or current selection</li>
3828 <li>disorder and secondary structure predictions
3829 available as dataset annotation</li>
3830 <li>Per-sequence rna helices colouring</li>
3833 <li>Sequence database accessions imported when fetching
3834 alignments from Rfam</li>
3835 <li>update VARNA version to 3.91</li>
3837 <li>New groovy scripts for exporting aligned positions,
3838 conservation values, and calculating sum of pairs scores.</li>
3839 <li>Command line argument to set default JABAWS server</li>
3840 <li>include installation type in build properties and
3841 console log output</li>
3842 <li>Updated Jalview project format to preserve dataset
3846 <!-- issues resolved --> <em>Application</em>
3848 <li>Distinguish alignment and sequence associated RNA
3849 structure in structure->view->VARNA</li>
3850 <li>Raise dialog box if user deletes all sequences in an
3852 <li>Pressing F1 results in documentation opening twice</li>
3853 <li>Sequence feature tooltip is wrapped</li>
3854 <li>Double click on sequence associated annotation
3855 selects only first column</li>
3856 <li>Redundancy removal doesn't result in unlinked
3857 leaves shown in tree</li>
3858 <li>Undos after several redundancy removals don't undo
3860 <li>Hide sequence doesn't hide associated annotation</li>
3861 <li>User defined colours dialog box too big to fit on
3862 screen and buttons not visible</li>
3863 <li>author list isn't updated if already written to
3864 Jalview properties</li>
3865 <li>Popup menu won't open after retrieving sequence
3867 <li>File open window for associate PDB doesn't open</li>
3868 <li>Left-then-right click on a sequence id opens a
3869 browser search window</li>
3870 <li>Cannot open sequence feature shading/sort popup menu
3871 in feature settings dialog</li>
3872 <li>better tooltip placement for some areas of Jalview
3874 <li>Allow addition of JABAWS Server which doesn't
3875 pass validation</li>
3876 <li>Web services parameters dialog box is too large to
3878 <li>Muscle nucleotide alignment preset obscured by
3880 <li>JABAWS preset submenus don't contain newly
3881 defined user preset</li>
3882 <li>MSA web services warns user if they were launched
3883 with invalid input</li>
3884 <li>Jalview cannot contact DAS Registy when running on
3887 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3888 'Superpose with' submenu not shown when new view
3892 </ul> <!-- <em>Applet</em>
3894 </ul> <em>General</em>
3896 </ul>--> <em>Deployment and Documentation</em>
3898 <li>2G and 1G options in launchApp have no effect on
3899 memory allocation</li>
3900 <li>launchApp service doesn't automatically open
3901 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3903 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3904 InstallAnywhere reports cannot find valid JVM when Java
3905 1.7_055 is available
3907 </ul> <em>Application Known issues</em>
3910 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3911 corrupted or unreadable alignment display when scrolling
3915 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3916 retrieval fails but progress bar continues for DAS retrieval
3917 with large number of ID
3920 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3921 flatfile output of visible region has incorrect sequence
3925 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3926 rna structure consensus doesn't update when secondary
3927 structure tracks are rearranged
3930 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3931 invalid rna structure positional highlighting does not
3932 highlight position of invalid base pairs
3935 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3936 out of memory errors are not raised when saving Jalview
3937 project from alignment window file menu
3940 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3941 Switching to RNA Helices colouring doesn't propagate to
3945 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3946 colour by RNA Helices not enabled when user created
3947 annotation added to alignment
3950 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3951 Jalview icon not shown on dock in Mountain Lion/Webstart
3953 </ul> <em>Applet Known Issues</em>
3956 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3957 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3960 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3961 Jalview and Jmol example not compatible with IE9
3964 <li>Sort by annotation score doesn't reverse order
3970 <td><div align="center">
3971 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3974 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3977 <li>Internationalisation of user interface (usually
3978 called i18n support) and translation for Spanish locale</li>
3979 <li>Define/Undefine group on current selection with
3980 Ctrl-G/Shift Ctrl-G</li>
3981 <li>Improved group creation/removal options in
3982 alignment/sequence Popup menu</li>
3983 <li>Sensible precision for symbol distribution
3984 percentages shown in logo tooltip.</li>
3985 <li>Annotation panel height set according to amount of
3986 annotation when alignment first opened</li>
3987 </ul> <em>Application</em>
3989 <li>Interactive consensus RNA secondary structure
3990 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3991 <li>Select columns containing particular features from
3992 Feature Settings dialog</li>
3993 <li>View all 'representative' PDB structures for selected
3995 <li>Update Jalview project format:
3997 <li>New file extension for Jalview projects '.jvp'</li>
3998 <li>Preserve sequence and annotation dataset (to
3999 store secondary structure annotation,etc)</li>
4000 <li>Per group and alignment annotation and RNA helix
4004 <li>New similarity measures for PCA and Tree calculation
4006 <li>Experimental support for retrieval and viewing of
4007 flanking regions for an alignment</li>
4011 <!-- issues resolved --> <em>Application</em>
4013 <li>logo keeps spinning and status remains at queued or
4014 running after job is cancelled</li>
4015 <li>cannot export features from alignments imported from
4016 Jalview/VAMSAS projects</li>
4017 <li>Buggy slider for web service parameters that take
4019 <li>Newly created RNA secondary structure line doesn't
4020 have 'display all symbols' flag set</li>
4021 <li>T-COFFEE alignment score shading scheme and other
4022 annotation shading not saved in Jalview project</li>
4023 <li>Local file cannot be loaded in freshly downloaded
4025 <li>Jalview icon not shown on dock in Mountain
4027 <li>Load file from desktop file browser fails</li>
4028 <li>Occasional NPE thrown when calculating large trees</li>
4029 <li>Cannot reorder or slide sequences after dragging an
4030 alignment onto desktop</li>
4031 <li>Colour by annotation dialog throws NPE after using
4032 'extract scores' function</li>
4033 <li>Loading/cut'n'pasting an empty file leads to a grey
4034 alignment window</li>
4035 <li>Disorder thresholds rendered incorrectly after
4036 performing IUPred disorder prediction</li>
4037 <li>Multiple group annotated consensus rows shown when
4038 changing 'normalise logo' display setting</li>
4039 <li>Find shows blank dialog after 'finished searching' if
4040 nothing matches query</li>
4041 <li>Null Pointer Exceptions raised when sorting by
4042 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4044 <li>Errors in Jmol console when structures in alignment
4045 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4047 <li>Not all working JABAWS services are shown in
4049 <li>JAVAWS version of Jalview fails to launch with
4050 'invalid literal/length code'</li>
4051 <li>Annotation/RNA Helix colourschemes cannot be applied
4052 to alignment with groups (actually fixed in 2.8.0b1)</li>
4053 <li>RNA Helices and T-Coffee Scores available as default
4056 </ul> <em>Applet</em>
4058 <li>Remove group option is shown even when selection is
4060 <li>Apply to all groups ticked but colourscheme changes
4061 don't affect groups</li>
4062 <li>Documented RNA Helices and T-Coffee Scores as valid
4063 colourscheme name</li>
4064 <li>Annotation labels drawn on sequence IDs when
4065 Annotation panel is not displayed</li>
4066 <li>Increased font size for dropdown menus on OSX and
4067 embedded windows</li>
4068 </ul> <em>Other</em>
4070 <li>Consensus sequence for alignments/groups with a
4071 single sequence were not calculated</li>
4072 <li>annotation files that contain only groups imported as
4073 annotation and junk sequences</li>
4074 <li>Fasta files with sequences containing '*' incorrectly
4075 recognised as PFAM or BLC</li>
4076 <li>conservation/PID slider apply all groups option
4077 doesn't affect background (2.8.0b1)
4079 <li>redundancy highlighting is erratic at 0% and 100%</li>
4080 <li>Remove gapped columns fails for sequences with ragged
4082 <li>AMSA annotation row with leading spaces is not
4083 registered correctly on import</li>
4084 <li>Jalview crashes when selecting PCA analysis for
4085 certain alignments</li>
4086 <li>Opening the colour by annotation dialog for an
4087 existing annotation based 'use original colours'
4088 colourscheme loses original colours setting</li>
4093 <td><div align="center">
4094 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4095 <em>30/1/2014</em></strong>
4099 <li>Trusted certificates for JalviewLite applet and
4100 Jalview Desktop application<br />Certificate was donated by
4101 <a href="https://www.certum.eu">Certum</a> to the Jalview
4102 open source project).
4104 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4105 <li>Output in Stockholm format</li>
4106 <li>Allow import of data from gzipped files</li>
4107 <li>Export/import group and sequence associated line
4108 graph thresholds</li>
4109 <li>Nucleotide substitution matrix that supports RNA and
4110 ambiguity codes</li>
4111 <li>Allow disorder predictions to be made on the current
4112 selection (or visible selection) in the same way that JPred
4114 <li>Groovy scripting for headless Jalview operation</li>
4115 </ul> <em>Other improvements</em>
4117 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4118 <li>COMBINE statement uses current SEQUENCE_REF and
4119 GROUP_REF scope to group annotation rows</li>
4120 <li>Support '' style escaping of quotes in Newick
4122 <li>Group options for JABAWS service by command line name</li>
4123 <li>Empty tooltip shown for JABA service options with a
4124 link but no description</li>
4125 <li>Select primary source when selecting authority in
4126 database fetcher GUI</li>
4127 <li>Add .mfa to FASTA file extensions recognised by
4129 <li>Annotation label tooltip text wrap</li>
4134 <li>Slow scrolling when lots of annotation rows are
4136 <li>Lots of NPE (and slowness) after creating RNA
4137 secondary structure annotation line</li>
4138 <li>Sequence database accessions not imported when
4139 fetching alignments from Rfam</li>
4140 <li>Incorrect SHMR submission for sequences with
4142 <li>View all structures does not always superpose
4144 <li>Option widgets in service parameters not updated to
4145 reflect user or preset settings</li>
4146 <li>Null pointer exceptions for some services without
4147 presets or adjustable parameters</li>
4148 <li>Discover PDB IDs entry in structure menu doesn't
4149 discover PDB xRefs</li>
4150 <li>Exception encountered while trying to retrieve
4151 features with DAS</li>
4152 <li>Lowest value in annotation row isn't coloured
4153 when colour by annotation (per sequence) is coloured</li>
4154 <li>Keyboard mode P jumps to start of gapped region when
4155 residue follows a gap</li>
4156 <li>Jalview appears to hang importing an alignment with
4157 Wrap as default or after enabling Wrap</li>
4158 <li>'Right click to add annotations' message
4159 shown in wrap mode when no annotations present</li>
4160 <li>Disorder predictions fail with NPE if no automatic
4161 annotation already exists on alignment</li>
4162 <li>oninit javascript function should be called after
4163 initialisation completes</li>
4164 <li>Remove redundancy after disorder prediction corrupts
4165 alignment window display</li>
4166 <li>Example annotation file in documentation is invalid</li>
4167 <li>Grouped line graph annotation rows are not exported
4168 to annotation file</li>
4169 <li>Multi-harmony analysis cannot be run when only two
4171 <li>Cannot create multiple groups of line graphs with
4172 several 'combine' statements in annotation file</li>
4173 <li>Pressing return several times causes Number Format
4174 exceptions in keyboard mode</li>
4175 <li>Multi-harmony (SHMMR) method doesn't submit
4176 correct partitions for input data</li>
4177 <li>Translation from DNA to Amino Acids fails</li>
4178 <li>Jalview fail to load newick tree with quoted label</li>
4179 <li>--headless flag isn't understood</li>
4180 <li>ClassCastException when generating EPS in headless
4182 <li>Adjusting sequence-associated shading threshold only
4183 changes one row's threshold</li>
4184 <li>Preferences and Feature settings panel panel
4185 doesn't open</li>
4186 <li>hide consensus histogram also hides conservation and
4187 quality histograms</li>
4192 <td><div align="center">
4193 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4195 <td><em>Application</em>
4197 <li>Support for JABAWS 2.0 Services (AACon alignment
4198 conservation, protein disorder and Clustal Omega)</li>
4199 <li>JABAWS server status indicator in Web Services
4201 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4202 in Jalview alignment window</li>
4203 <li>Updated Jalview build and deploy framework for OSX
4204 mountain lion, windows 7, and 8</li>
4205 <li>Nucleotide substitution matrix for PCA that supports
4206 RNA and ambiguity codes</li>
4208 <li>Improved sequence database retrieval GUI</li>
4209 <li>Support fetching and database reference look up
4210 against multiple DAS sources (Fetch all from in 'fetch db
4212 <li>Jalview project improvements
4214 <li>Store and retrieve the 'belowAlignment'
4215 flag for annotation</li>
4216 <li>calcId attribute to group annotation rows on the
4218 <li>Store AACon calculation settings for a view in
4219 Jalview project</li>
4223 <li>horizontal scrolling gesture support</li>
4224 <li>Visual progress indicator when PCA calculation is
4226 <li>Simpler JABA web services menus</li>
4227 <li>visual indication that web service results are still
4228 being retrieved from server</li>
4229 <li>Serialise the dialogs that are shown when Jalview
4230 starts up for first time</li>
4231 <li>Jalview user agent string for interacting with HTTP
4233 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4235 <li>Examples directory and Groovy library included in
4236 InstallAnywhere distribution</li>
4237 </ul> <em>Applet</em>
4239 <li>RNA alignment and secondary structure annotation
4240 visualization applet example</li>
4241 </ul> <em>General</em>
4243 <li>Normalise option for consensus sequence logo</li>
4244 <li>Reset button in PCA window to return dimensions to
4246 <li>Allow seqspace or Jalview variant of alignment PCA
4248 <li>PCA with either nucleic acid and protein substitution
4250 <li>Allow windows containing HTML reports to be exported
4252 <li>Interactive display and editing of RNA secondary
4253 structure contacts</li>
4254 <li>RNA Helix Alignment Colouring</li>
4255 <li>RNA base pair logo consensus</li>
4256 <li>Parse sequence associated secondary structure
4257 information in Stockholm files</li>
4258 <li>HTML Export database accessions and annotation
4259 information presented in tooltip for sequences</li>
4260 <li>Import secondary structure from LOCARNA clustalw
4261 style RNA alignment files</li>
4262 <li>import and visualise T-COFFEE quality scores for an
4264 <li>'colour by annotation' per sequence option to
4265 shade each sequence according to its associated alignment
4267 <li>New Jalview Logo</li>
4268 </ul> <em>Documentation and Development</em>
4270 <li>documentation for score matrices used in Jalview</li>
4271 <li>New Website!</li>
4273 <td><em>Application</em>
4275 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4276 wsdbfetch REST service</li>
4277 <li>Stop windows being moved outside desktop on OSX</li>
4278 <li>Filetype associations not installed for webstart
4280 <li>Jalview does not always retrieve progress of a JABAWS
4281 job execution in full once it is complete</li>
4282 <li>revise SHMR RSBS definition to ensure alignment is
4283 uploaded via ali_file parameter</li>
4284 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4285 <li>View all structures superposed fails with exception</li>
4286 <li>Jnet job queues forever if a very short sequence is
4287 submitted for prediction</li>
4288 <li>Cut and paste menu not opened when mouse clicked on
4290 <li>Putting fractional value into integer text box in
4291 alignment parameter dialog causes Jalview to hang</li>
4292 <li>Structure view highlighting doesn't work on
4294 <li>View all structures fails with exception shown in
4296 <li>Characters in filename associated with PDBEntry not
4297 escaped in a platform independent way</li>
4298 <li>Jalview desktop fails to launch with exception when
4300 <li>Tree calculation reports 'you must have 2 or more
4301 sequences selected' when selection is empty</li>
4302 <li>Jalview desktop fails to launch with jar signature
4303 failure when java web start temporary file caching is
4305 <li>DAS Sequence retrieval with range qualification
4306 results in sequence xref which includes range qualification</li>
4307 <li>Errors during processing of command line arguments
4308 cause progress bar (JAL-898) to be removed</li>
4309 <li>Replace comma for semi-colon option not disabled for
4310 DAS sources in sequence fetcher</li>
4311 <li>Cannot close news reader when JABAWS server warning
4312 dialog is shown</li>
4313 <li>Option widgets not updated to reflect user settings</li>
4314 <li>Edited sequence not submitted to web service</li>
4315 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4316 <li>InstallAnywhere installer doesn't unpack and run
4317 on OSX Mountain Lion</li>
4318 <li>Annotation panel not given a scroll bar when
4319 sequences with alignment annotation are pasted into the
4321 <li>Sequence associated annotation rows not associated
4322 when loaded from Jalview project</li>
4323 <li>Browser launch fails with NPE on java 1.7</li>
4324 <li>JABAWS alignment marked as finished when job was
4325 cancelled or job failed due to invalid input</li>
4326 <li>NPE with v2.7 example when clicking on Tree
4327 associated with all views</li>
4328 <li>Exceptions when copy/paste sequences with grouped
4329 annotation rows to new window</li>
4330 </ul> <em>Applet</em>
4332 <li>Sequence features are momentarily displayed before
4333 they are hidden using hidefeaturegroups applet parameter</li>
4334 <li>loading features via javascript API automatically
4335 enables feature display</li>
4336 <li>scrollToColumnIn javascript API method doesn't
4338 </ul> <em>General</em>
4340 <li>Redundancy removal fails for rna alignment</li>
4341 <li>PCA calculation fails when sequence has been selected
4342 and then deselected</li>
4343 <li>PCA window shows grey box when first opened on OSX</li>
4344 <li>Letters coloured pink in sequence logo when alignment
4345 coloured with clustalx</li>
4346 <li>Choosing fonts without letter symbols defined causes
4347 exceptions and redraw errors</li>
4348 <li>Initial PCA plot view is not same as manually
4349 reconfigured view</li>
4350 <li>Grouped annotation graph label has incorrect line
4352 <li>Grouped annotation graph label display is corrupted
4353 for lots of labels</li>
4358 <div align="center">
4359 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4362 <td><em>Application</em>
4364 <li>Jalview Desktop News Reader</li>
4365 <li>Tweaked default layout of web services menu</li>
4366 <li>View/alignment association menu to enable user to
4367 easily specify which alignment a multi-structure view takes
4368 its colours/correspondences from</li>
4369 <li>Allow properties file location to be specified as URL</li>
4370 <li>Extend Jalview project to preserve associations
4371 between many alignment views and a single Jmol display</li>
4372 <li>Store annotation row height in Jalview project file</li>
4373 <li>Annotation row column label formatting attributes
4374 stored in project file</li>
4375 <li>Annotation row order for auto-calculated annotation
4376 rows preserved in Jalview project file</li>
4377 <li>Visual progress indication when Jalview state is
4378 saved using Desktop window menu</li>
4379 <li>Visual indication that command line arguments are
4380 still being processed</li>
4381 <li>Groovy script execution from URL</li>
4382 <li>Colour by annotation default min and max colours in
4384 <li>Automatically associate PDB files dragged onto an
4385 alignment with sequences that have high similarity and
4387 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4388 <li>'view structures' option to open many
4389 structures in same window</li>
4390 <li>Sort associated views menu option for tree panel</li>
4391 <li>Group all JABA and non-JABA services for a particular
4392 analysis function in its own submenu</li>
4393 </ul> <em>Applet</em>
4395 <li>Userdefined and autogenerated annotation rows for
4397 <li>Adjustment of alignment annotation pane height</li>
4398 <li>Annotation scrollbar for annotation panel</li>
4399 <li>Drag to reorder annotation rows in annotation panel</li>
4400 <li>'automaticScrolling' parameter</li>
4401 <li>Allow sequences with partial ID string matches to be
4402 annotated from GFF/Jalview features files</li>
4403 <li>Sequence logo annotation row in applet</li>
4404 <li>Absolute paths relative to host server in applet
4405 parameters are treated as such</li>
4406 <li>New in the JalviewLite javascript API:
4408 <li>JalviewLite.js javascript library</li>
4409 <li>Javascript callbacks for
4411 <li>Applet initialisation</li>
4412 <li>Sequence/alignment mouse-overs and selections</li>
4415 <li>scrollTo row and column alignment scrolling
4417 <li>Select sequence/alignment regions from javascript</li>
4418 <li>javascript structure viewer harness to pass
4419 messages between Jmol and Jalview when running as
4420 distinct applets</li>
4421 <li>sortBy method</li>
4422 <li>Set of applet and application examples shipped
4423 with documentation</li>
4424 <li>New example to demonstrate JalviewLite and Jmol
4425 javascript message exchange</li>
4427 </ul> <em>General</em>
4429 <li>Enable Jmol displays to be associated with multiple
4430 multiple alignments</li>
4431 <li>Option to automatically sort alignment with new tree</li>
4432 <li>User configurable link to enable redirects to a
4433 www.Jalview.org mirror</li>
4434 <li>Jmol colours option for Jmol displays</li>
4435 <li>Configurable newline string when writing alignment
4436 and other flat files</li>
4437 <li>Allow alignment annotation description lines to
4438 contain html tags</li>
4439 </ul> <em>Documentation and Development</em>
4441 <li>Add groovy test harness for bulk load testing to
4443 <li>Groovy script to load and align a set of sequences
4444 using a web service before displaying the result in the
4445 Jalview desktop</li>
4446 <li>Restructured javascript and applet api documentation</li>
4447 <li>Ant target to publish example html files with applet
4449 <li>Netbeans project for building Jalview from source</li>
4450 <li>ant task to create online javadoc for Jalview source</li>
4452 <td><em>Application</em>
4454 <li>User defined colourscheme throws exception when
4455 current built in colourscheme is saved as new scheme</li>
4456 <li>AlignFrame->Save in application pops up save
4457 dialog for valid filename/format</li>
4458 <li>Cannot view associated structure for UniProt sequence</li>
4459 <li>PDB file association breaks for UniProt sequence
4461 <li>Associate PDB from file dialog does not tell you
4462 which sequence is to be associated with the file</li>
4463 <li>Find All raises null pointer exception when query
4464 only matches sequence IDs</li>
4465 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4466 <li>Jalview project with Jmol views created with Jalview
4467 2.4 cannot be loaded</li>
4468 <li>Filetype associations not installed for webstart
4470 <li>Two or more chains in a single PDB file associated
4471 with sequences in different alignments do not get coloured
4472 by their associated sequence</li>
4473 <li>Visibility status of autocalculated annotation row
4474 not preserved when project is loaded</li>
4475 <li>Annotation row height and visibility attributes not
4476 stored in Jalview project</li>
4477 <li>Tree bootstraps are not preserved when saved as a
4478 Jalview project</li>
4479 <li>Envision2 workflow tooltips are corrupted</li>
4480 <li>Enabling show group conservation also enables colour
4481 by conservation</li>
4482 <li>Duplicate group associated conservation or consensus
4483 created on new view</li>
4484 <li>Annotation scrollbar not displayed after 'show
4485 all hidden annotation rows' option selected</li>
4486 <li>Alignment quality not updated after alignment
4487 annotation row is hidden then shown</li>
4488 <li>Preserve colouring of structures coloured by
4489 sequences in pre Jalview 2.7 projects</li>
4490 <li>Web service job parameter dialog is not laid out
4492 <li>Web services menu not refreshed after 'reset
4493 services' button is pressed in preferences</li>
4494 <li>Annotation off by one in Jalview v2_3 example project</li>
4495 <li>Structures imported from file and saved in project
4496 get name like jalview_pdb1234.txt when reloaded</li>
4497 <li>Jalview does not always retrieve progress of a JABAWS
4498 job execution in full once it is complete</li>
4499 </ul> <em>Applet</em>
4501 <li>Alignment height set incorrectly when lots of
4502 annotation rows are displayed</li>
4503 <li>Relative URLs in feature HTML text not resolved to
4505 <li>View follows highlighting does not work for positions
4507 <li><= shown as = in tooltip</li>
4508 <li>Export features raises exception when no features
4510 <li>Separator string used for serialising lists of IDs
4511 for javascript api is modified when separator string
4512 provided as parameter</li>
4513 <li>Null pointer exception when selecting tree leaves for
4514 alignment with no existing selection</li>
4515 <li>Relative URLs for datasources assumed to be relative
4516 to applet's codebase</li>
4517 <li>Status bar not updated after finished searching and
4518 search wraps around to first result</li>
4519 <li>StructureSelectionManager instance shared between
4520 several Jalview applets causes race conditions and memory
4522 <li>Hover tooltip and mouseover of position on structure
4523 not sent from Jmol in applet</li>
4524 <li>Certain sequences of javascript method calls to
4525 applet API fatally hang browser</li>
4526 </ul> <em>General</em>
4528 <li>View follows structure mouseover scrolls beyond
4529 position with wrapped view and hidden regions</li>
4530 <li>Find sequence position moves to wrong residue
4531 with/without hidden columns</li>
4532 <li>Sequence length given in alignment properties window
4534 <li>InvalidNumberFormat exceptions thrown when trying to
4535 import PDB like structure files</li>
4536 <li>Positional search results are only highlighted
4537 between user-supplied sequence start/end bounds</li>
4538 <li>End attribute of sequence is not validated</li>
4539 <li>Find dialog only finds first sequence containing a
4540 given sequence position</li>
4541 <li>Sequence numbering not preserved in MSF alignment
4543 <li>Jalview PDB file reader does not extract sequence
4544 from nucleotide chains correctly</li>
4545 <li>Structure colours not updated when tree partition
4546 changed in alignment</li>
4547 <li>Sequence associated secondary structure not correctly
4548 parsed in interleaved stockholm</li>
4549 <li>Colour by annotation dialog does not restore current
4551 <li>Hiding (nearly) all sequences doesn't work
4553 <li>Sequences containing lowercase letters are not
4554 properly associated with their pdb files</li>
4555 </ul> <em>Documentation and Development</em>
4557 <li>schemas/JalviewWsParamSet.xsd corrupted by
4558 ApplyCopyright tool</li>
4563 <div align="center">
4564 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4567 <td><em>Application</em>
4569 <li>New warning dialog when the Jalview Desktop cannot
4570 contact web services</li>
4571 <li>JABA service parameters for a preset are shown in
4572 service job window</li>
4573 <li>JABA Service menu entries reworded</li>
4577 <li>Modeller PIR IO broken - cannot correctly import a
4578 pir file emitted by Jalview</li>
4579 <li>Existing feature settings transferred to new
4580 alignment view created from cut'n'paste</li>
4581 <li>Improved test for mixed amino/nucleotide chains when
4582 parsing PDB files</li>
4583 <li>Consensus and conservation annotation rows
4584 occasionally become blank for all new windows</li>
4585 <li>Exception raised when right clicking above sequences
4586 in wrapped view mode</li>
4587 </ul> <em>Application</em>
4589 <li>multiple multiply aligned structure views cause cpu
4590 usage to hit 100% and computer to hang</li>
4591 <li>Web Service parameter layout breaks for long user
4592 parameter names</li>
4593 <li>Jaba service discovery hangs desktop if Jaba server
4600 <div align="center">
4601 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4604 <td><em>Application</em>
4606 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4607 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4610 <li>Web Services preference tab</li>
4611 <li>Analysis parameters dialog box and user defined
4613 <li>Improved speed and layout of Envision2 service menu</li>
4614 <li>Superpose structures using associated sequence
4616 <li>Export coordinates and projection as CSV from PCA
4618 </ul> <em>Applet</em>
4620 <li>enable javascript: execution by the applet via the
4621 link out mechanism</li>
4622 </ul> <em>Other</em>
4624 <li>Updated the Jmol Jalview interface to work with Jmol
4626 <li>The Jalview Desktop and JalviewLite applet now
4627 require Java 1.5</li>
4628 <li>Allow Jalview feature colour specification for GFF
4629 sequence annotation files</li>
4630 <li>New 'colour by label' keword in Jalview feature file
4631 type colour specification</li>
4632 <li>New Jalview Desktop Groovy API method that allows a
4633 script to check if it being run in an interactive session or
4634 in a batch operation from the Jalview command line</li>
4638 <li>clustalx colourscheme colours Ds preferentially when
4639 both D+E are present in over 50% of the column</li>
4640 </ul> <em>Application</em>
4642 <li>typo in AlignmentFrame->View->Hide->all but
4643 selected Regions menu item</li>
4644 <li>sequence fetcher replaces ',' for ';' when the ',' is
4645 part of a valid accession ID</li>
4646 <li>fatal OOM if object retrieved by sequence fetcher
4647 runs out of memory</li>
4648 <li>unhandled Out of Memory Error when viewing pca
4649 analysis results</li>
4650 <li>InstallAnywhere builds fail to launch on OS X java
4651 10.5 update 4 (due to apple Java 1.6 update)</li>
4652 <li>Installanywhere Jalview silently fails to launch</li>
4653 </ul> <em>Applet</em>
4655 <li>Jalview.getFeatureGroups() raises an
4656 ArrayIndexOutOfBoundsException if no feature groups are
4663 <div align="center">
4664 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4670 <li>Alignment prettyprinter doesn't cope with long
4672 <li>clustalx colourscheme colours Ds preferentially when
4673 both D+E are present in over 50% of the column</li>
4674 <li>nucleic acid structures retrieved from PDB do not
4675 import correctly</li>
4676 <li>More columns get selected than were clicked on when a
4677 number of columns are hidden</li>
4678 <li>annotation label popup menu not providing correct
4679 add/hide/show options when rows are hidden or none are
4681 <li>Stockholm format shown in list of readable formats,
4682 and parser copes better with alignments from RFAM.</li>
4683 <li>CSV output of consensus only includes the percentage
4684 of all symbols if sequence logo display is enabled</li>
4686 </ul> <em>Applet</em>
4688 <li>annotation panel disappears when annotation is
4690 </ul> <em>Application</em>
4692 <li>Alignment view not redrawn properly when new
4693 alignment opened where annotation panel is visible but no
4694 annotations are present on alignment</li>
4695 <li>pasted region containing hidden columns is
4696 incorrectly displayed in new alignment window</li>
4697 <li>Jalview slow to complete operations when stdout is
4698 flooded (fix is to close the Jalview console)</li>
4699 <li>typo in AlignmentFrame->View->Hide->all but
4700 selected Rregions menu item.</li>
4701 <li>inconsistent group submenu and Format submenu entry
4702 'Un' or 'Non'conserved</li>
4703 <li>Sequence feature settings are being shared by
4704 multiple distinct alignments</li>
4705 <li>group annotation not recreated when tree partition is
4707 <li>double click on group annotation to select sequences
4708 does not propagate to associated trees</li>
4709 <li>Mac OSX specific issues:
4711 <li>exception raised when mouse clicked on desktop
4712 window background</li>
4713 <li>Desktop menu placed on menu bar and application
4714 name set correctly</li>
4715 <li>sequence feature settings not wide enough for the
4716 save feature colourscheme button</li>
4725 <div align="center">
4726 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4729 <td><em>New Capabilities</em>
4731 <li>URL links generated from description line for
4732 regular-expression based URL links (applet and application)
4735 <li>Non-positional feature URL links are shown in link
4737 <li>Linked viewing of nucleic acid sequences and
4739 <li>Automatic Scrolling option in View menu to display
4740 the currently highlighted region of an alignment.</li>
4741 <li>Order an alignment by sequence length, or using the
4742 average score or total feature count for each sequence.</li>
4743 <li>Shading features by score or associated description</li>
4744 <li>Subdivide alignment and groups based on identity of
4745 selected subsequence (Make Groups from Selection).</li>
4746 <li>New hide/show options including Shift+Control+H to
4747 hide everything but the currently selected region.</li>
4748 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4749 </ul> <em>Application</em>
4751 <li>Fetch DB References capabilities and UI expanded to
4752 support retrieval from DAS sequence sources</li>
4753 <li>Local DAS Sequence sources can be added via the
4754 command line or via the Add local source dialog box.</li>
4755 <li>DAS Dbref and DbxRef feature types are parsed as
4756 database references and protein_name is parsed as
4757 description line (BioSapiens terms).</li>
4758 <li>Enable or disable non-positional feature and database
4759 references in sequence ID tooltip from View menu in
4761 <!-- <li>New hidden columns and rows and representatives capabilities
4762 in annotations file (in progress - not yet fully implemented)</li> -->
4763 <li>Group-associated consensus, sequence logos and
4764 conservation plots</li>
4765 <li>Symbol distributions for each column can be exported
4766 and visualized as sequence logos</li>
4767 <li>Optionally scale multi-character column labels to fit
4768 within each column of annotation row<!-- todo for applet -->
4770 <li>Optional automatic sort of associated alignment view
4771 when a new tree is opened.</li>
4772 <li>Jalview Java Console</li>
4773 <li>Better placement of desktop window when moving
4774 between different screens.</li>
4775 <li>New preference items for sequence ID tooltip and
4776 consensus annotation</li>
4777 <li>Client to submit sequences and IDs to Envision2
4779 <li><em>Vamsas Capabilities</em>
4781 <li>Improved VAMSAS synchronization (Jalview archive
4782 used to preserve views, structures, and tree display
4784 <li>Import of vamsas documents from disk or URL via
4786 <li>Sharing of selected regions between views and
4787 with other VAMSAS applications (Experimental feature!)</li>
4788 <li>Updated API to VAMSAS version 0.2</li>
4790 </ul> <em>Applet</em>
4792 <li>Middle button resizes annotation row height</li>
4795 <li>sortByTree (true/false) - automatically sort the
4796 associated alignment view by the tree when a new tree is
4798 <li>showTreeBootstraps (true/false) - show or hide
4799 branch bootstraps (default is to show them if available)</li>
4800 <li>showTreeDistances (true/false) - show or hide
4801 branch lengths (default is to show them if available)</li>
4802 <li>showUnlinkedTreeNodes (true/false) - indicate if
4803 unassociated nodes should be highlighted in the tree
4805 <li>heightScale and widthScale (1.0 or more) -
4806 increase the height or width of a cell in the alignment
4807 grid relative to the current font size.</li>
4810 <li>Non-positional features displayed in sequence ID
4812 </ul> <em>Other</em>
4814 <li>Features format: graduated colour definitions and
4815 specification of feature scores</li>
4816 <li>Alignment Annotations format: new keywords for group
4817 associated annotation (GROUP_REF) and annotation row display
4818 properties (ROW_PROPERTIES)</li>
4819 <li>XML formats extended to support graduated feature
4820 colourschemes, group associated annotation, and profile
4821 visualization settings.</li></td>
4824 <li>Source field in GFF files parsed as feature source
4825 rather than description</li>
4826 <li>Non-positional features are now included in sequence
4827 feature and gff files (controlled via non-positional feature
4828 visibility in tooltip).</li>
4829 <li>URL links generated for all feature links (bugfix)</li>
4830 <li>Added URL embedding instructions to features file
4832 <li>Codons containing ambiguous nucleotides translated as
4833 'X' in peptide product</li>
4834 <li>Match case switch in find dialog box works for both
4835 sequence ID and sequence string and query strings do not
4836 have to be in upper case to match case-insensitively.</li>
4837 <li>AMSA files only contain first column of
4838 multi-character column annotation labels</li>
4839 <li>Jalview Annotation File generation/parsing consistent
4840 with documentation (e.g. Stockholm annotation can be
4841 exported and re-imported)</li>
4842 <li>PDB files without embedded PDB IDs given a friendly
4844 <li>Find incrementally searches ID string matches as well
4845 as subsequence matches, and correctly reports total number
4849 <li>Better handling of exceptions during sequence
4851 <li>Dasobert generated non-positional feature URL
4852 link text excludes the start_end suffix</li>
4853 <li>DAS feature and source retrieval buttons disabled
4854 when fetch or registry operations in progress.</li>
4855 <li>PDB files retrieved from URLs are cached properly</li>
4856 <li>Sequence description lines properly shared via
4858 <li>Sequence fetcher fetches multiple records for all
4860 <li>Ensured that command line das feature retrieval
4861 completes before alignment figures are generated.</li>
4862 <li>Reduced time taken when opening file browser for
4864 <li>isAligned check prior to calculating tree, PCA or
4865 submitting an MSA to JNet now excludes hidden sequences.</li>
4866 <li>User defined group colours properly recovered
4867 from Jalview projects.</li>
4876 <div align="center">
4877 <strong>2.4.0.b2</strong><br> 28/10/2009
4882 <li>Experimental support for google analytics usage
4884 <li>Jalview privacy settings (user preferences and docs).</li>
4889 <li>Race condition in applet preventing startup in
4891 <li>Exception when feature created from selection beyond
4892 length of sequence.</li>
4893 <li>Allow synthetic PDB files to be imported gracefully</li>
4894 <li>Sequence associated annotation rows associate with
4895 all sequences with a given id</li>
4896 <li>Find function matches case-insensitively for sequence
4897 ID string searches</li>
4898 <li>Non-standard characters do not cause pairwise
4899 alignment to fail with exception</li>
4900 </ul> <em>Application Issues</em>
4902 <li>Sequences are now validated against EMBL database</li>
4903 <li>Sequence fetcher fetches multiple records for all
4905 </ul> <em>InstallAnywhere Issues</em>
4907 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4908 issue with installAnywhere mechanism)</li>
4909 <li>Command line launching of JARs from InstallAnywhere
4910 version (java class versioning error fixed)</li>
4917 <div align="center">
4918 <strong>2.4</strong><br> 27/8/2008
4921 <td><em>User Interface</em>
4923 <li>Linked highlighting of codon and amino acid from
4924 translation and protein products</li>
4925 <li>Linked highlighting of structure associated with
4926 residue mapping to codon position</li>
4927 <li>Sequence Fetcher provides example accession numbers
4928 and 'clear' button</li>
4929 <li>MemoryMonitor added as an option under Desktop's
4931 <li>Extract score function to parse whitespace separated
4932 numeric data in description line</li>
4933 <li>Column labels in alignment annotation can be centred.</li>
4934 <li>Tooltip for sequence associated annotation give name
4936 </ul> <em>Web Services and URL fetching</em>
4938 <li>JPred3 web service</li>
4939 <li>Prototype sequence search client (no public services
4941 <li>Fetch either seed alignment or full alignment from
4943 <li>URL Links created for matching database cross
4944 references as well as sequence ID</li>
4945 <li>URL Links can be created using regular-expressions</li>
4946 </ul> <em>Sequence Database Connectivity</em>
4948 <li>Retrieval of cross-referenced sequences from other
4950 <li>Generalised database reference retrieval and
4951 validation to all fetchable databases</li>
4952 <li>Fetch sequences from DAS sources supporting the
4953 sequence command</li>
4954 </ul> <em>Import and Export</em>
4955 <li>export annotation rows as CSV for spreadsheet import</li>
4956 <li>Jalview projects record alignment dataset associations,
4957 EMBL products, and cDNA sequence mappings</li>
4958 <li>Sequence Group colour can be specified in Annotation
4960 <li>Ad-hoc colouring of group in Annotation File using RGB
4961 triplet as name of colourscheme</li>
4962 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4964 <li>treenode binding for VAMSAS tree exchange</li>
4965 <li>local editing and update of sequences in VAMSAS
4966 alignments (experimental)</li>
4967 <li>Create new or select existing session to join</li>
4968 <li>load and save of vamsas documents</li>
4969 </ul> <em>Application command line</em>
4971 <li>-tree parameter to open trees (introduced for passing
4973 <li>-fetchfrom command line argument to specify nicknames
4974 of DAS servers to query for alignment features</li>
4975 <li>-dasserver command line argument to add new servers
4976 that are also automatically queried for features</li>
4977 <li>-groovy command line argument executes a given groovy
4978 script after all input data has been loaded and parsed</li>
4979 </ul> <em>Applet-Application data exchange</em>
4981 <li>Trees passed as applet parameters can be passed to
4982 application (when using "View in full
4983 application")</li>
4984 </ul> <em>Applet Parameters</em>
4986 <li>feature group display control parameter</li>
4987 <li>debug parameter</li>
4988 <li>showbutton parameter</li>
4989 </ul> <em>Applet API methods</em>
4991 <li>newView public method</li>
4992 <li>Window (current view) specific get/set public methods</li>
4993 <li>Feature display control methods</li>
4994 <li>get list of currently selected sequences</li>
4995 </ul> <em>New Jalview distribution features</em>
4997 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4998 <li>RELEASE file gives build properties for the latest
4999 Jalview release.</li>
5000 <li>Java 1.1 Applet build made easier and donotobfuscate
5001 property controls execution of obfuscator</li>
5002 <li>Build target for generating source distribution</li>
5003 <li>Debug flag for javacc</li>
5004 <li>.jalview_properties file is documented (slightly) in
5005 jalview.bin.Cache</li>
5006 <li>Continuous Build Integration for stable and
5007 development version of Application, Applet and source
5012 <li>selected region output includes visible annotations
5013 (for certain formats)</li>
5014 <li>edit label/displaychar contains existing label/char
5016 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5017 <li>shorter peptide product names from EMBL records</li>
5018 <li>Newick string generator makes compact representations</li>
5019 <li>bootstrap values parsed correctly for tree files with
5021 <li>pathological filechooser bug avoided by not allowing
5022 filenames containing a ':'</li>
5023 <li>Fixed exception when parsing GFF files containing
5024 global sequence features</li>
5025 <li>Alignment datasets are finalized only when number of
5026 references from alignment sequences goes to zero</li>
5027 <li>Close of tree branch colour box without colour
5028 selection causes cascading exceptions</li>
5029 <li>occasional negative imgwidth exceptions</li>
5030 <li>better reporting of non-fatal warnings to user when
5031 file parsing fails.</li>
5032 <li>Save works when Jalview project is default format</li>
5033 <li>Save as dialog opened if current alignment format is
5034 not a valid output format</li>
5035 <li>UniProt canonical names introduced for both das and
5037 <li>Histidine should be midblue (not pink!) in Zappo</li>
5038 <li>error messages passed up and output when data read
5040 <li>edit undo recovers previous dataset sequence when
5041 sequence is edited</li>
5042 <li>allow PDB files without pdb ID HEADER lines (like
5043 those generated by MODELLER) to be read in properly</li>
5044 <li>allow reading of JPred concise files as a normal
5046 <li>Stockholm annotation parsing and alignment properties
5047 import fixed for PFAM records</li>
5048 <li>Structure view windows have correct name in Desktop
5050 <li>annotation consisting of sequence associated scores
5051 can be read and written correctly to annotation file</li>
5052 <li>Aligned cDNA translation to aligned peptide works
5054 <li>Fixed display of hidden sequence markers and
5055 non-italic font for representatives in Applet</li>
5056 <li>Applet Menus are always embedded in applet window on
5058 <li>Newly shown features appear at top of stack (in
5060 <li>Annotations added via parameter not drawn properly
5061 due to null pointer exceptions</li>
5062 <li>Secondary structure lines are drawn starting from
5063 first column of alignment</li>
5064 <li>UniProt XML import updated for new schema release in
5066 <li>Sequence feature to sequence ID match for Features
5067 file is case-insensitive</li>
5068 <li>Sequence features read from Features file appended to
5069 all sequences with matching IDs</li>
5070 <li>PDB structure coloured correctly for associated views
5071 containing a sub-sequence</li>
5072 <li>PDB files can be retrieved by applet from Jar files</li>
5073 <li>feature and annotation file applet parameters
5074 referring to different directories are retrieved correctly</li>
5075 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5076 <li>Fixed application hang whilst waiting for
5077 splash-screen version check to complete</li>
5078 <li>Applet properly URLencodes input parameter values
5079 when passing them to the launchApp service</li>
5080 <li>display name and local features preserved in results
5081 retrieved from web service</li>
5082 <li>Visual delay indication for sequence retrieval and
5083 sequence fetcher initialisation</li>
5084 <li>updated Application to use DAS 1.53e version of
5085 dasobert DAS client</li>
5086 <li>Re-instated Full AMSA support and .amsa file
5088 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5096 <div align="center">
5097 <strong>2.3</strong><br> 9/5/07
5102 <li>Jmol 11.0.2 integration</li>
5103 <li>PDB views stored in Jalview XML files</li>
5104 <li>Slide sequences</li>
5105 <li>Edit sequence in place</li>
5106 <li>EMBL CDS features</li>
5107 <li>DAS Feature mapping</li>
5108 <li>Feature ordering</li>
5109 <li>Alignment Properties</li>
5110 <li>Annotation Scores</li>
5111 <li>Sort by scores</li>
5112 <li>Feature/annotation editing in applet</li>
5117 <li>Headless state operation in 2.2.1</li>
5118 <li>Incorrect and unstable DNA pairwise alignment</li>
5119 <li>Cut and paste of sequences with annotation</li>
5120 <li>Feature group display state in XML</li>
5121 <li>Feature ordering in XML</li>
5122 <li>blc file iteration selection using filename # suffix</li>
5123 <li>Stockholm alignment properties</li>
5124 <li>Stockhom alignment secondary structure annotation</li>
5125 <li>2.2.1 applet had no feature transparency</li>
5126 <li>Number pad keys can be used in cursor mode</li>
5127 <li>Structure Viewer mirror image resolved</li>
5134 <div align="center">
5135 <strong>2.2.1</strong><br> 12/2/07
5140 <li>Non standard characters can be read and displayed
5141 <li>Annotations/Features can be imported/exported to the
5143 <li>Applet allows editing of sequence/annotation/group
5144 name & description
5145 <li>Preference setting to display sequence name in
5147 <li>Annotation file format extended to allow
5148 Sequence_groups to be defined
5149 <li>Default opening of alignment overview panel can be
5150 specified in preferences
5151 <li>PDB residue numbering annotation added to associated
5157 <li>Applet crash under certain Linux OS with Java 1.6
5159 <li>Annotation file export / import bugs fixed
5160 <li>PNG / EPS image output bugs fixed
5166 <div align="center">
5167 <strong>2.2</strong><br> 27/11/06
5172 <li>Multiple views on alignment
5173 <li>Sequence feature editing
5174 <li>"Reload" alignment
5175 <li>"Save" to current filename
5176 <li>Background dependent text colour
5177 <li>Right align sequence ids
5178 <li>User-defined lower case residue colours
5181 <li>Menu item accelerator keys
5182 <li>Control-V pastes to current alignment
5183 <li>Cancel button for DAS Feature Fetching
5184 <li>PCA and PDB Viewers zoom via mouse roller
5185 <li>User-defined sub-tree colours and sub-tree selection
5188 <li>'New Window' button on the 'Output to Text box'
5193 <li>New memory efficient Undo/Redo System
5194 <li>Optimised symbol lookups and conservation/consensus
5196 <li>Region Conservation/Consensus recalculated after
5198 <li>Fixed Remove Empty Columns Bug (empty columns at end
5200 <li>Slowed DAS Feature Fetching for increased robustness.
5203 <li>Made angle brackets in ASCII feature descriptions
5205 <li>Re-instated Zoom function for PCA
5206 <li>Sequence descriptions conserved in web service
5208 <li>UniProt ID discoverer uses any word separated by
5210 <li>WsDbFetch query/result association resolved
5211 <li>Tree leaf to sequence mapping improved
5212 <li>Smooth fonts switch moved to FontChooser dialog box.
5220 <div align="center">
5221 <strong>2.1.1</strong><br> 12/9/06
5226 <li>Copy consensus sequence to clipboard</li>
5231 <li>Image output - rightmost residues are rendered if
5232 sequence id panel has been resized</li>
5233 <li>Image output - all offscreen group boundaries are
5235 <li>Annotation files with sequence references - all
5236 elements in file are relative to sequence position</li>
5237 <li>Mac Applet users can use Alt key for group editing</li>
5243 <div align="center">
5244 <strong>2.1</strong><br> 22/8/06
5249 <li>MAFFT Multiple Alignment in default Web Service list</li>
5250 <li>DAS Feature fetching</li>
5251 <li>Hide sequences and columns</li>
5252 <li>Export Annotations and Features</li>
5253 <li>GFF file reading / writing</li>
5254 <li>Associate structures with sequences from local PDB
5256 <li>Add sequences to exisiting alignment</li>
5257 <li>Recently opened files / URL lists</li>
5258 <li>Applet can launch the full application</li>
5259 <li>Applet has transparency for features (Java 1.2
5261 <li>Applet has user defined colours parameter</li>
5262 <li>Applet can load sequences from parameter
5263 "sequence<em>x</em>"
5269 <li>Redundancy Panel reinstalled in the Applet</li>
5270 <li>Monospaced font - EPS / rescaling bug fixed</li>
5271 <li>Annotation files with sequence references bug fixed</li>
5277 <div align="center">
5278 <strong>2.08.1</strong><br> 2/5/06
5283 <li>Change case of selected region from Popup menu</li>
5284 <li>Choose to match case when searching</li>
5285 <li>Middle mouse button and mouse movement can compress /
5286 expand the visible width and height of the alignment</li>
5291 <li>Annotation Panel displays complete JNet results</li>
5297 <div align="center">
5298 <strong>2.08b</strong><br> 18/4/06
5304 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5305 <li>Righthand label on wrapped alignments shows correct
5312 <div align="center">
5313 <strong>2.08</strong><br> 10/4/06
5318 <li>Editing can be locked to the selection area</li>
5319 <li>Keyboard editing</li>
5320 <li>Create sequence features from searches</li>
5321 <li>Precalculated annotations can be loaded onto
5323 <li>Features file allows grouping of features</li>
5324 <li>Annotation Colouring scheme added</li>
5325 <li>Smooth fonts off by default - Faster rendering</li>
5326 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5331 <li>Drag & Drop fixed on Linux</li>
5332 <li>Jalview Archive file faster to load/save, sequence
5333 descriptions saved.</li>
5339 <div align="center">
5340 <strong>2.07</strong><br> 12/12/05
5345 <li>PDB Structure Viewer enhanced</li>
5346 <li>Sequence Feature retrieval and display enhanced</li>
5347 <li>Choose to output sequence start-end after sequence
5348 name for file output</li>
5349 <li>Sequence Fetcher WSDBFetch@EBI</li>
5350 <li>Applet can read feature files, PDB files and can be
5351 used for HTML form input</li>
5356 <li>HTML output writes groups and features</li>
5357 <li>Group editing is Control and mouse click</li>
5358 <li>File IO bugs</li>
5364 <div align="center">
5365 <strong>2.06</strong><br> 28/9/05
5370 <li>View annotations in wrapped mode</li>
5371 <li>More options for PCA viewer</li>
5376 <li>GUI bugs resolved</li>
5377 <li>Runs with -nodisplay from command line</li>
5383 <div align="center">
5384 <strong>2.05b</strong><br> 15/9/05
5389 <li>Choose EPS export as lineart or text</li>
5390 <li>Jar files are executable</li>
5391 <li>Can read in Uracil - maps to unknown residue</li>
5396 <li>Known OutOfMemory errors give warning message</li>
5397 <li>Overview window calculated more efficiently</li>
5398 <li>Several GUI bugs resolved</li>
5404 <div align="center">
5405 <strong>2.05</strong><br> 30/8/05
5410 <li>Edit and annotate in "Wrapped" view</li>
5415 <li>Several GUI bugs resolved</li>
5421 <div align="center">
5422 <strong>2.04</strong><br> 24/8/05
5427 <li>Hold down mouse wheel & scroll to change font
5433 <li>Improved JPred client reliability</li>
5434 <li>Improved loading of Jalview files</li>
5440 <div align="center">
5441 <strong>2.03</strong><br> 18/8/05
5446 <li>Set Proxy server name and port in preferences</li>
5447 <li>Multiple URL links from sequence ids</li>
5448 <li>User Defined Colours can have a scheme name and added
5450 <li>Choose to ignore gaps in consensus calculation</li>
5451 <li>Unix users can set default web browser</li>
5452 <li>Runs without GUI for batch processing</li>
5453 <li>Dynamically generated Web Service Menus</li>
5458 <li>InstallAnywhere download for Sparc Solaris</li>
5464 <div align="center">
5465 <strong>2.02</strong><br> 18/7/05
5471 <li>Copy & Paste order of sequences maintains
5472 alignment order.</li>
5478 <div align="center">
5479 <strong>2.01</strong><br> 12/7/05
5484 <li>Use delete key for deleting selection.</li>
5485 <li>Use Mouse wheel to scroll sequences.</li>
5486 <li>Help file updated to describe how to add alignment
5488 <li>Version and build date written to build properties
5490 <li>InstallAnywhere installation will check for updates
5491 at launch of Jalview.</li>
5496 <li>Delete gaps bug fixed.</li>
5497 <li>FileChooser sorts columns.</li>
5498 <li>Can remove groups one by one.</li>
5499 <li>Filechooser icons installed.</li>
5500 <li>Finder ignores return character when searching.
5501 Return key will initiate a search.<br>
5508 <div align="center">
5509 <strong>2.0</strong><br> 20/6/05
5514 <li>New codebase</li>